I run verify and repair after a system crash (sleep-related). It finds 2 missing. Repair does fix the issue. How can I find out which two files are missing?
I encountered this a few months ago, also with two missing. I accepted this, and a few days later I noted it was coming up clean.
Those 2 files got orphaned, meaning they exist inside DT’s file system but DT forgot they are there when the index got corrupted (maybe during an interrupted disk operation). You can probably get them back if you open the database file (reveal package contents from Finder and search for them inside the folder “files.noindex”). Drag them out with a copy operation (not a move) and reimport. Do not modify the database file in any way while outside DT.