fix: ignore duplicate matches whose file is gone

The hash lives in the database and the file does not, so a file deleted behind
the app's back went on refusing its own replacement. Matches are now checked
against disk, and re-adding a book's own missing file writes it back into the
row that already describes it.

backend/AGENTS.md

@@ -128,9 +128,18 @@ The policy differs by how deliberate the import is:
 | `create_many_from_existing_files` (consume watcher) | Skips, and **moves the file to `CHITAI_DUPLICATE_PATH/<library slug>/`** — nothing is deleted, and it cannot stay put because `watchfiles` only reports additions. That path must stay outside `consume_path` or the watcher re-imports it and tries to read the directory name as a library slug. |
 
 `allow_duplicates=true` overrides all of it, on every endpoint. Keep that working — the
-hash is not proof of identity, so a false positive has to be recoverable.
+hash is not proof of identity, so a wrong verdict has to be recoverable, and a scripted
+import needs a way through. The **web UI deliberately does not offer it**: storing the
+same bytes twice splits reading progress and shelf membership across two records that
+can never converge, which is nothing anyone wants on purpose.
 
-Two things to preserve when touching this code:
+Three things to preserve when touching this code:
+
+- **A match only counts while the file is on disk.** `find_duplicate_files` stats each
+  candidate, and `add_files` writes a missing file back into the row that already
+  describes it (`_restore_file`) instead of adding a second row beside it. The hash
+  lives in the database and the file does not, so without this a file deleted behind
+  the app's back would go on refusing its own replacement.
 
 - **Screening runs before anything is written.** `fingerprint_upload` reads the spooled
   upload and rewinds it; the resulting fingerprints are handed to `_save_book_files`,