@bmeddings - calibre is 'driven' by the content of its library database (metadata.db), not the subfolders and files within the library folder, however it does require that the latter to match with the database.
If you mess with the contents of the library folder with something like Total Commander's synchronisation feature (or anything similar), its almost certain to break the nexus between the database and file system folders and files. The golden rule with calibre library sub-folders and files is 'look but don't touch'.
Before doing anything else I recommend you use the calibre's
Check library tool:-
Click OK/Yes on the messages and you will get to a dialogue that looks like this:-
The Help panel on the right explains the different error types, and what sort of corrections (Fix/Delete) can be done from that screen. After using the Fix and Delete options the Copy to clipboard can be used to get a hard copy of the remaining errors.
A simple way to 'sort out' the remaining errors is to use calibre's Copy to Library (delete after copy) feature to copy all the books from the existing library (oldLibrary) to a fresh library (newLibrary). The oldLibrary will then contain books that need to handled 'manually'. You could use Add books to add the books in the oldLibrary to the newLibrary using this option:-
Now you will have a clean library that you can 'compare' with the backup libraries using Find Duplicates->Find library duplicates.
I recommend you steer clear of the calibre library folders when you're in Total Commander, if you want to see what's in a book folder from calibre press 'O'.
I also recommend you run the check Library regularly, I run it before I do my weekly backups. Normally there are no errors, on the odd occasion there is one I can invariably account for it as a blunder on my part.
BR