AFAIK using the wrong method to transfer is a sure-fire method to lose metadata YOU added. Using
Add Books to transfer to another Library. That reads the BOOK for metadata. If you did not Polish or Embed metadata, the filed (Library stored) version is pretty much as it was added originally.
Metadata is inside the DB. This is why you MUST use Calibre for most things.
Only Calibre changes the DB.
The user tells Calibre to do things. If you use something non-Calibre aware to make partial (file or folder) changes. Calibre is kept in the dark and loses sync with where it put things.
While I distrust "Otto"
doing transfers, I can't believe it would change relative locations of files (mix things up).
"Oh! this metadata.db is newer (Library 2), so I will replace the older one (belongs to Library 1) BTW that should produce way more errors unless it was from an older backup, where the books were still named exactly the same.
Calibre uses 2 (file system) Locations (1 Library Users) for data. The Library folder and the User settings (configuration) folder . The Configuration does NOT contain Book Specific Metadata.
Something rebuilt the DB WITHOUT using the Recovery data kept with each Library and Book. (the JSON file in the Library folder has the DB Structure. Metadata.opf, WITH in the Title folder) has the data for that books entry.)