A file doesn’t go empty but empty files are sometimes created by some applications. Some of them are valid; some not. For example, if an image is zero-byte (empty), there’s something clearly wrong with it. DEVONthink checks for common valid types and ignores them. It warns of others.
You can’t merge missing files in a database. And you must curate those files - missing or empty. This is the general procedure for handling them.
- Clear Window > Log.
- Do a File > Verify & Repair on the database.
- Press Repair when prompted.
- Press Ok in the next dialog.
- Check Window > Log for empty or missing files.
- Control-click a result and choose Reveal if you’d like to see where the file resides in the database. Then use the Move to Trash option.
- If you don’t need the file, then use the Move to Trash option.
- If you do need the file, you’ll need to find a copy of the file and reimport it.
This may involve restoring the database from your backups, opening the restored copy, and moving files between the restored and current database. When you’re done, delete the restored database so you don’t have two of the same database in the system.
- Empty the database’s Trash to remove the files.
- Do a File > Verify & Repair Database to check if it’s healthy now.
- Repeat the steps with other databases as needed.
Actually, doing a File > Rebuild Database will purge references to missing files in case someone saw they weren’t of any use.