Each Library is a self contained set of files and folders. the files BetterRed controls the interface (what you see). These are a lock stepped SET, which is why you do not change things OUTSIDE of the Calibre GUI or CLI.
If something keeps disappearing, you had a storage / AV issue.
You mentioned a 1T flash. There are a lot of fakes (reports way larger than the chip stores). I suspect you metadata.db's are getting stomped upon
Also Flash can fail with no notice. Usually HD's start making small errors that should be taken as a warning :"clone me now"