I had a chance to look at the SQLite database you sent to me. It appears there are only 29 tracks in crates in the library. Of those, only one of them has a corresponding entry in the library table. It looks to me like all the others were somehow deleted from the library table.
I’m not sure how this happened. There is only one way that the code could have removed these rows from the library table and that is by using the “Purge Tracks” feature present in 1.10.x. You said you were only using Mixxx 1.9.x so I’m pretty stumped.
Using a simple heuristic I think I may have reconstructed which tracks those were. Could you check your email? I’ve emailed you crate / track pairings. If you can confirm that those are the right pairings I can try to re-construct those crates if you’d like.