If you use the OS to change any filename or folder, Calibre will 'lose track' of them. Don't mess under the skirts
Restore uses the metadata.OPF file. I believe it also
assumes 
that the file reflects its current FILE SYSTEM position. if you messed... the OPF is stale (invalid)
Dual Boot (Win - Linux) can introduce Path Case issues.
Do read the Calibre Help: FAQ section