First update to latest
calibre, then run library maintenance, you will have to do manual fixes for most of the problems.
Suggestion copy the library to a new library keeping current settings, then remove all books from the original library, check the old library with file manager, any folders books left in the old library need to be checked to see if they where copied over to the new.
Make backups before you start.
bernie
P.S.
I just copied my library from my mint 17 pc to a windows 10 tablet.