diff --git a/backend/alembic/versions/0077_add_platform_fs_name_index.py b/backend/alembic/versions/0077_add_platform_fs_name_index.py
new file mode 100644
index 000000000..03fcba159
--- /dev/null
+++ b/backend/alembic/versions/0077_add_platform_fs_name_index.py
@@ -0,0 +1,29 @@
+"""Add composite index on (platform_id, fs_name) for roms table
+
+Revision ID: 0077_add_platform_fs_name_index
+Revises: 0076_play_sessions
+Create Date: 2026-04-11 00:00:00.000000
+
+"""
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "0077_add_platform_fs_name_index"
+down_revision = "0076_play_sessions"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    with op.batch_alter_table("roms", schema=None) as batch_op:
+        batch_op.create_index(
+            "idx_roms_platform_id_fs_name",
+            ["platform_id", "fs_name"],
+            unique=False,
+        )
+
+
+def downgrade() -> None:
+    with op.batch_alter_table("roms", schema=None) as batch_op:
+        batch_op.drop_index("idx_roms_platform_id_fs_name")
diff --git a/backend/endpoints/sockets/scan.py b/backend/endpoints/sockets/scan.py
index 9b0579aa5..e65aa86a2 100644
--- a/backend/endpoints/sockets/scan.py
+++ b/backend/endpoints/sockets/scan.py
@@ -243,20 +243,6 @@ async def _identify_rom(
     if redis_client.get(STOP_SCAN_FLAG):
         return
 
-    if not _should_scan_rom(
-        scan_type=scan_type,
-        rom=rom,
-        roms_ids=roms_ids,
-        metadata_sources=metadata_sources,
-    ):
-        if rom:
-            # Just to update the filesystem data
-            db_rom_handler.update_rom(
-                rom.id, {"fs_name": fs_rom["fs_name"], "missing_from_fs": False}
-            )
-
-        return
-
     # Update properties that don't require metadata
     parsed_tags = fs_rom_handler.parse_tags(fs_rom["fs_name"])
     roms_path = fs_rom_handler.get_roms_fs_structure(platform.fs_slug)
@@ -465,6 +451,7 @@ async def _identify_platform(
     socket_manager: socketio.AsyncRedisManager,
     scan_stats: ScanStats,
     calculate_hashes: bool = True,
+    fs_roms_cache: dict[str, list[FSRom]] | None = None,
 ) -> ScanStats:
     # Stop the scan if the flag is set
     if redis_client.get(STOP_SCAN_FLAG):
@@ -533,12 +520,15 @@ async def _identify_platform(
         new_firmware=new_firmware,
     )
 
-    # Scanning roms
-    try:
-        fs_roms = await fs_rom_handler.get_roms(platform)
-    except RomsNotFoundException as e:
-        log.error(e)
-        return scan_stats
+    # Scanning roms — use cached filesystem data if available
+    if fs_roms_cache is not None and platform_slug in fs_roms_cache:
+        fs_roms = fs_roms_cache[platform_slug]
+    else:
+        try:
+            fs_roms = await fs_rom_handler.get_roms(platform)
+        except RomsNotFoundException as e:
+            log.error(e)
+            return scan_stats
 
     if len(fs_roms) == 0:
         log.warning(
@@ -572,19 +562,41 @@ async def _identify_platform(
             fs_names={fs_rom["fs_name"] for fs_rom in fs_roms_batch},
         )
 
-        # Process ROMs concurrently within the batch
-        scan_tasks = [
-            scan_rom_with_semaphore(
-                fs_rom=fs_rom, rom=roms_by_fs_name.get(fs_rom["fs_name"])
+        # Separate skipped ROMs from those that need scanning
+        skipped_rom_ids: list[int] = []
+        roms_to_scan: list[tuple[FSRom, Rom | None]] = []
+
+        for fs_rom in fs_roms_batch:
+            rom = roms_by_fs_name.get(fs_rom["fs_name"])
+            if _should_scan_rom(
+                scan_type=scan_type,
+                rom=rom,
+                roms_ids=roms_ids,
+                metadata_sources=metadata_sources,
+            ):
+                roms_to_scan.append((fs_rom, rom))
+            elif rom:
+                skipped_rom_ids.append(rom.id)
+
+        # Bulk update all skipped ROMs in one query instead of per-ROM updates
+        if skipped_rom_ids:
+            db_rom_handler.bulk_mark_present(platform.id, skipped_rom_ids)
+            await scan_stats.increment(
+                socket_manager=socket_manager,
+                scanned_roms=len(skipped_rom_ids),
             )
-            for fs_rom in fs_roms_batch
+
+        # Process only ROMs that actually need scanning
+        scan_tasks = [
+            scan_rom_with_semaphore(fs_rom=fs_rom, rom=rom)
+            for fs_rom, rom in roms_to_scan
         ]
 
-        # Wait for all ROMs in the batch to complete
-        batched_results = await asyncio.gather(*scan_tasks, return_exceptions=True)
-        for result, fs_rom in zip(batched_results, fs_roms_batch, strict=False):
-            if isinstance(result, Exception):
-                log.error(f"Error scanning ROM {fs_rom['fs_name']}: {result}")
+        if scan_tasks:
+            batched_results = await asyncio.gather(*scan_tasks, return_exceptions=True)
+            for result, (fs_rom, _) in zip(batched_results, roms_to_scan, strict=False):
+                if isinstance(result, Exception):
+                    log.error(f"Error scanning ROM {fs_rom['fs_name']}: {result}")
 
     missing_roms = db_rom_handler.mark_missing_roms(
         platform.id, [rom["fs_name"] for rom in fs_roms]
@@ -645,11 +657,14 @@ async def scan_platforms(
     if MetadataSource.HLTB in metadata_sources:
         meta_hltb_handler.initialize()
 
-    # Precalculate total platforms and ROMs
+    # Precalculate total platforms and ROMs, caching filesystem reads
+    # so _identify_platform() doesn't have to re-read the same directories
+    fs_roms_cache: dict[str, list[FSRom]] = {}
     total_roms = 0
     for platform_slug in fs_platforms:
         try:
             fs_roms = await fs_rom_handler.get_roms(Platform(fs_slug=platform_slug))
+            fs_roms_cache[platform_slug] = fs_roms
             total_roms += len(fs_roms)
         except RomsNotFoundException as e:
             log.error(e)
@@ -694,6 +709,7 @@ async def scan_platforms(
                 socket_manager=socket_manager,
                 scan_stats=scan_stats,
                 calculate_hashes=calculate_hashes,
+                fs_roms_cache=fs_roms_cache,
             )
 
         missed_platforms = db_platform_handler.mark_missing_platforms(fs_platforms)
diff --git a/backend/handler/database/roms_handler.py b/backend/handler/database/roms_handler.py
index d161162fd..d71c23ccf 100644
--- a/backend/handler/database/roms_handler.py
+++ b/backend/handler/database/roms_handler.py
@@ -922,7 +922,6 @@ class DBRomsHandler(DBBaseHandler):
         )
 
     @begin_session
-    @with_details
     def get_roms_by_fs_name(
         self,
         platform_id: int,
@@ -966,6 +965,31 @@ class DBRomsHandler(DBBaseHandler):
             .execution_options(synchronize_session="evaluate")
         )
 
+    @begin_session
+    def bulk_mark_present(
+        self,
+        platform_id: int,
+        rom_ids: list[int],
+        session: Session = None,  # type: ignore
+    ) -> None:
+        """Bulk set missing_from_fs=False for a list of ROM IDs."""
+        if not rom_ids:
+            return
+
+        for i in range(0, len(rom_ids), 1000):
+            chunk = rom_ids[i : i + 1000]
+            session.execute(
+                update(Rom)
+                .where(
+                    and_(
+                        Rom.platform_id == platform_id,
+                        Rom.id.in_(chunk),
+                    )
+                )
+                .values(missing_from_fs=False)
+                .execution_options(synchronize_session="evaluate")
+            )
+
     @begin_session
     def mark_missing_roms(
         self,
@@ -973,30 +997,46 @@ class DBRomsHandler(DBBaseHandler):
         fs_roms_to_keep: list[str],
         session: Session = None,  # type: ignore
     ) -> Sequence[Rom]:
+        # Mark ALL ROMs for this platform as missing
+        session.execute(
+            update(Rom)
+            .where(Rom.platform_id == platform_id)
+            .values(missing_from_fs=True)
+            .execution_options(synchronize_session="evaluate")
+        )
+
+        # Un-mark ROMs that exist on filesystem (in chunks)
+        for i in range(0, len(fs_roms_to_keep), 1000):
+            chunk = fs_roms_to_keep[i : i + 1000]
+            session.execute(
+                update(Rom)
+                .where(
+                    and_(
+                        Rom.platform_id == platform_id,
+                        Rom.fs_name.in_(chunk),
+                    )
+                )
+                .values(missing_from_fs=False)
+                .execution_options(synchronize_session="evaluate")
+            )
+
+        # Return the ones that remained marked as missing (for logging)
         missing_roms = (
             session.scalars(
                 select(Rom)
+                .options(load_only(Rom.id, Rom.fs_name))
                 .order_by(Rom.fs_name.asc())
                 .where(
                     and_(
                         Rom.platform_id == platform_id,
-                        Rom.fs_name.not_in(fs_roms_to_keep),
+                        Rom.missing_from_fs.is_(True),
                     )
                 )
             )
             .unique()
             .all()
         )
-        session.execute(
-            update(Rom)
-            .where(
-                and_(
-                    Rom.platform_id == platform_id, Rom.fs_name.not_in(fs_roms_to_keep)
-                )
-            )
-            .values(**{"missing_from_fs": True})
-            .execution_options(synchronize_session="evaluate")
-        )
+
         return missing_roms
 
     @begin_session
diff --git a/backend/models/rom.py b/backend/models/rom.py
index 3ff51ec06..37bbe5928 100644
--- a/backend/models/rom.py
+++ b/backend/models/rom.py
@@ -173,6 +173,7 @@ class Rom(BaseModel):
         Index("idx_roms_flashpoint_id", "flashpoint_id"),
         Index("idx_roms_hltb_id", "hltb_id"),
         Index("idx_roms_gamelist_id", "gamelist_id"),
+        Index("idx_roms_platform_id_fs_name", "platform_id", "fs_name"),
     )
 
     fs_name: Mapped[str] = mapped_column(String(length=FILE_NAME_MAX_LENGTH))
diff --git a/backend/tests/handler/test_db_handler.py b/backend/tests/handler/test_db_handler.py
index fbeb6e544..9ef7537d9 100644
--- a/backend/tests/handler/test_db_handler.py
+++ b/backend/tests/handler/test_db_handler.py
@@ -340,6 +340,298 @@ def test_article_stripping_sort(platform: Platform):
     assert [r.name for r in roms] == ["The Legend", "A Quest", "Zelda"]
 
 
+def test_bulk_mark_present(platform: Platform):
+    """bulk_mark_present sets missing_from_fs=False for the given ROM IDs."""
+    roms = []
+    for i in range(5):
+        rom = db_rom_handler.add_rom(
+            Rom(
+                platform_id=platform.id,
+                name=f"rom_{i}",
+                slug=f"rom-{i}",
+                fs_name=f"rom_{i}.zip",
+                fs_name_no_tags=f"rom_{i}",
+                fs_name_no_ext=f"rom_{i}",
+                fs_extension="zip",
+                fs_path=f"{platform.slug}/roms",
+                missing_from_fs=True,
+            )
+        )
+        roms.append(rom)
+
+    # Mark first 3 as present
+    db_rom_handler.bulk_mark_present(platform.id, [r.id for r in roms[:3]])
+
+    for r in roms[:3]:
+        updated = db_rom_handler.get_rom(r.id)
+        assert updated is not None
+        assert updated.missing_from_fs is False
+
+    for r in roms[3:]:
+        updated = db_rom_handler.get_rom(r.id)
+        assert updated is not None
+        assert updated.missing_from_fs is True
+
+
+def test_bulk_mark_present_empty_list(platform: Platform):
+    """bulk_mark_present with an empty list is a no-op."""
+    rom = db_rom_handler.add_rom(
+        Rom(
+            platform_id=platform.id,
+            name="rom_lonely",
+            slug="rom-lonely",
+            fs_name="rom_lonely.zip",
+            fs_name_no_tags="rom_lonely",
+            fs_name_no_ext="rom_lonely",
+            fs_extension="zip",
+            fs_path=f"{platform.slug}/roms",
+            missing_from_fs=True,
+        )
+    )
+
+    db_rom_handler.bulk_mark_present(platform.id, [])
+
+    updated = db_rom_handler.get_rom(rom.id)
+    assert updated is not None
+    assert updated.missing_from_fs is True
+
+
+def test_bulk_mark_present_chunking(platform: Platform):
+    """bulk_mark_present handles >1000 IDs via internal chunking."""
+    roms = []
+    for i in range(1050):
+        rom = db_rom_handler.add_rom(
+            Rom(
+                platform_id=platform.id,
+                name=f"rom_{i}",
+                slug=f"rom-{i}",
+                fs_name=f"rom_{i}.zip",
+                fs_name_no_tags=f"rom_{i}",
+                fs_name_no_ext=f"rom_{i}",
+                fs_extension="zip",
+                fs_path=f"{platform.slug}/roms",
+                missing_from_fs=True,
+            )
+        )
+        roms.append(rom)
+
+    all_ids = [r.id for r in roms]
+    db_rom_handler.bulk_mark_present(platform.id, all_ids)
+
+    # Spot-check a few across chunk boundaries
+    for idx in [0, 999, 1000, 1049]:
+        updated = db_rom_handler.get_rom(roms[idx].id)
+        assert updated is not None
+        assert updated.missing_from_fs is False
+
+
+def test_mark_missing_roms_small_platform(platform: Platform):
+    """mark_missing_roms correctly identifies missing ROMs with a small keep list."""
+    rom_a = db_rom_handler.add_rom(
+        Rom(
+            platform_id=platform.id,
+            name="rom_a",
+            slug="rom-a",
+            fs_name="rom_a.zip",
+            fs_name_no_tags="rom_a",
+            fs_name_no_ext="rom_a",
+            fs_extension="zip",
+            fs_path=f"{platform.slug}/roms",
+        )
+    )
+    rom_b = db_rom_handler.add_rom(
+        Rom(
+            platform_id=platform.id,
+            name="rom_b",
+            slug="rom-b",
+            fs_name="rom_b.zip",
+            fs_name_no_tags="rom_b",
+            fs_name_no_ext="rom_b",
+            fs_extension="zip",
+            fs_path=f"{platform.slug}/roms",
+        )
+    )
+    rom_c = db_rom_handler.add_rom(
+        Rom(
+            platform_id=platform.id,
+            name="rom_c",
+            slug="rom-c",
+            fs_name="rom_c.zip",
+            fs_name_no_tags="rom_c",
+            fs_name_no_ext="rom_c",
+            fs_extension="zip",
+            fs_path=f"{platform.slug}/roms",
+        )
+    )
+
+    # Keep only rom_a and rom_c
+    missing = db_rom_handler.mark_missing_roms(platform.id, ["rom_a.zip", "rom_c.zip"])
+
+    assert len(missing) == 1
+    assert missing[0].fs_name == "rom_b.zip"
+
+    updated_b = db_rom_handler.get_rom(rom_b.id)
+    assert updated_b is not None
+    assert updated_b.missing_from_fs is True
+
+    updated_a = db_rom_handler.get_rom(rom_a.id)
+    assert updated_a is not None
+    assert updated_a.missing_from_fs is False
+
+
+def test_mark_missing_roms_large_platform(platform: Platform):
+    """mark_missing_roms correctly identifies missing ROMs with a large keep list."""
+    rom_present = db_rom_handler.add_rom(
+        Rom(
+            platform_id=platform.id,
+            name="rom_present",
+            slug="rom-present",
+            fs_name="rom_present.zip",
+            fs_name_no_tags="rom_present",
+            fs_name_no_ext="rom_present",
+            fs_extension="zip",
+            fs_path=f"{platform.slug}/roms",
+        )
+    )
+    rom_missing = db_rom_handler.add_rom(
+        Rom(
+            platform_id=platform.id,
+            name="rom_missing",
+            slug="rom-missing",
+            fs_name="rom_missing.zip",
+            fs_name_no_tags="rom_missing",
+            fs_name_no_ext="rom_missing",
+            fs_extension="zip",
+            fs_path=f"{platform.slug}/roms",
+        )
+    )
+
+    # Build a keep list with >500 entries to trigger the flip-based path.
+    # Only rom_present.zip actually exists in DB; the rest are just filler.
+    fs_roms_to_keep = ["rom_present.zip"] + [f"filler_{i}.zip" for i in range(501)]
+
+    missing = db_rom_handler.mark_missing_roms(platform.id, fs_roms_to_keep)
+
+    assert len(missing) == 1
+    assert missing[0].fs_name == "rom_missing.zip"
+
+    updated_present = db_rom_handler.get_rom(rom_present.id)
+    assert updated_present is not None
+    assert updated_present.missing_from_fs is False
+
+    updated_missing = db_rom_handler.get_rom(rom_missing.id)
+    assert updated_missing is not None
+    assert updated_missing.missing_from_fs is True
+
+
+def test_mark_missing_roms_large_platform_all_present(platform: Platform):
+    """When all ROMs are in the keep list, none should be marked missing."""
+    roms = []
+    for i in range(3):
+        rom = db_rom_handler.add_rom(
+            Rom(
+                platform_id=platform.id,
+                name=f"rom_{i}",
+                slug=f"rom-{i}",
+                fs_name=f"rom_{i}.zip",
+                fs_name_no_tags=f"rom_{i}",
+                fs_name_no_ext=f"rom_{i}",
+                fs_extension="zip",
+                fs_path=f"{platform.slug}/roms",
+            )
+        )
+        roms.append(rom)
+
+    # Keep list has all real ROMs plus filler to exceed 500
+    fs_roms_to_keep = [f"rom_{i}.zip" for i in range(3)] + [
+        f"filler_{i}.zip" for i in range(500)
+    ]
+
+    missing = db_rom_handler.mark_missing_roms(platform.id, fs_roms_to_keep)
+    assert len(missing) == 0
+
+    for rom in roms:
+        updated = db_rom_handler.get_rom(rom.id)
+        assert updated is not None
+        assert updated.missing_from_fs is False
+
+
+def test_mark_missing_roms_large_platform_all_missing(platform: Platform):
+    """When no ROMs are in the keep list, all should be marked missing."""
+    roms = []
+    for i in range(3):
+        rom = db_rom_handler.add_rom(
+            Rom(
+                platform_id=platform.id,
+                name=f"rom_{i}",
+                slug=f"rom-{i}",
+                fs_name=f"rom_{i}.zip",
+                fs_name_no_tags=f"rom_{i}",
+                fs_name_no_ext=f"rom_{i}",
+                fs_extension="zip",
+                fs_path=f"{platform.slug}/roms",
+            )
+        )
+        roms.append(rom)
+
+    # Keep list has only filler — none of the real ROMs
+    fs_roms_to_keep = [f"filler_{i}.zip" for i in range(501)]
+
+    missing = db_rom_handler.mark_missing_roms(platform.id, fs_roms_to_keep)
+    assert len(missing) == 3
+
+    missing_names = {r.fs_name for r in missing}
+    assert missing_names == {"rom_0.zip", "rom_1.zip", "rom_2.zip"}
+
+
+def test_mark_missing_roms_does_not_affect_other_platforms(platform: Platform):
+    """mark_missing_roms should only affect ROMs on the target platform."""
+    other_platform = db_platform_handler.add_platform(
+        Platform(
+            name="other_platform",
+            slug="other_platform_slug",
+            fs_slug="other_platform_slug",
+        )
+    )
+
+    rom_on_target = db_rom_handler.add_rom(
+        Rom(
+            platform_id=platform.id,
+            name="target_rom",
+            slug="target-rom",
+            fs_name="target_rom.zip",
+            fs_name_no_tags="target_rom",
+            fs_name_no_ext="target_rom",
+            fs_extension="zip",
+            fs_path=f"{platform.slug}/roms",
+        )
+    )
+    rom_on_other = db_rom_handler.add_rom(
+        Rom(
+            platform_id=other_platform.id,
+            name="other_rom",
+            slug="other-rom",
+            fs_name="other_rom.zip",
+            fs_name_no_tags="other_rom",
+            fs_name_no_ext="other_rom",
+            fs_extension="zip",
+            fs_path=f"{other_platform.slug}/roms",
+        )
+    )
+
+    # Use flip-based path (>500 items), keeping nothing on target platform
+    fs_roms_to_keep = [f"filler_{i}.zip" for i in range(501)]
+    missing = db_rom_handler.mark_missing_roms(platform.id, fs_roms_to_keep)
+
+    assert len(missing) == 1
+    assert missing[0].fs_name == "target_rom.zip"
+
+    # Other platform's ROM should be untouched
+    updated_other = db_rom_handler.get_rom(rom_on_other.id)
+    assert updated_other is not None
+    assert updated_other.missing_from_fs is False
+
+
 def test_users(admin_user):
     db_user_handler.add_user(
         User(