diff --git a/prisma/migrations/20260722000000_mark_retained_manual_files/migration.sql b/prisma/migrations/20260722000000_mark_retained_manual_files/migration.sql
new file mode 100644
index 0000000..b2b1ca8
--- /dev/null
+++ b/prisma/migrations/20260722000000_mark_retained_manual_files/migration.sql
@@ -0,0 +1 @@
+ALTER TABLE "manual_upload_files" ADD COLUMN "retainedAt" TIMESTAMP(3);
diff --git a/prisma/schema.prisma b/prisma/schema.prisma
index 679a74e..ce14213 100644
--- a/prisma/schema.prisma
+++ b/prisma/schema.prisma
@@ -937,6 +937,7 @@ model ManualUploadFile {
   filePath        String       // Path on shared volume
   fileSize        BigInt
   packageId       String?      // Set after processing
+  retainedAt      DateTime?
 
   upload          ManualUpload @relation(fields: [uploadId], references: [id], onDelete: Cascade)
 
diff --git a/scripts/backup/restore.sh b/scripts/backup/restore.sh
index 3085baa..d96621a 100755
--- a/scripts/backup/restore.sh
+++ b/scripts/backup/restore.sh
@@ -180,12 +180,25 @@ verify_file_references() {
   local database_user="${POSTGRES_USER:-dragons}"
   local database_name="${POSTGRES_DB:-dragonsstash}"
   docker compose exec -T db psql --no-psqlrc --tuples-only --no-align --quiet \
+    --field-separator=$'\t' \
     --username "$database_user" --dbname "$database_name" \
-    --command 'SELECT "filePath" FROM "manual_upload_files" ORDER BY "filePath"' |
+    --command "SELECT 'legacy', \"filePath\" FROM \"manual_upload_files\" WHERE \"retainedAt\" IS NULL
+      UNION ALL
+      SELECT 'retained', \"filePath\" FROM \"manual_upload_files\" WHERE \"retainedAt\" IS NOT NULL
+      ORDER BY 2" |
     docker compose --profile backup run --rm --no-deps -T --entrypoint bash \
       -v "$uploads_volume:/data/uploads:ro" backup -ceu '
         missing=0
-        while IFS= read -r file_path; do
+        while IFS="$(printf "\t")" read -r retention file_path; do
+          if [[ "$retention" == "legacy" ]]; then
+            printf "Warning: legacy manual-upload file reference is not required because retainedAt is NULL: %s\\n" "$file_path" >&2
+            continue
+          fi
+          if [[ "$retention" != "retained" ]]; then
+            printf "Unexpected retention status for database reference: %s\\n" "$file_path" >&2
+            missing=1
+            continue
+          fi
           case "$file_path" in
             /data/uploads/*) relative_path="${file_path#/data/uploads/}" ;;
             *)
diff --git a/src/app/api/uploads/route.ts b/src/app/api/uploads/route.ts
index 225abee..4f9cc30 100644
--- a/src/app/api/uploads/route.ts
+++ b/src/app/api/uploads/route.ts
@@ -55,6 +55,7 @@ export async function POST(request: Request) {
           fileName: file.name,
           filePath,
           fileSize: BigInt(file.size),
+          retainedAt: new Date(),
         },
       });
     }
diff --git a/worker/src/manual-upload.ts b/worker/src/manual-upload.ts
index 3cef614..1757261 100644
--- a/worker/src/manual-upload.ts
+++ b/worker/src/manual-upload.ts
@@ -1,4 +1,3 @@
-import path from "path";
 import { rm } from "fs/promises";
 import { db } from "./db/client.js";
 import { childLogger } from "./util/logger.js";
@@ -200,12 +199,4 @@ export async function processManualUpload(uploadId: string): Promise<void> {
       data: { status: "FAILED", errorMessage: message },
     });
   }
-
-  // Clean up uploaded files
-  try {
-    const uploadDir = path.join("/data/uploads", uploadId);
-    await rm(uploadDir, { recursive: true, force: true });
-  } catch {
-    // Best-effort cleanup
-  }
 }