[Adoby]

If it is the same books, with the same names and the same folder structure, but from different points in time, you could use Midnight Commander to copy both trees to the same new overlapping location.

When asked if you want to write over existing files specify update so you only write over if newer.

The "cp" command can do the same using -R for recursive and -u for update.

One complication could be that you may end up with duplicates with very similar names. This is because SMB/CIFS has a different case sensitivity compared to most Linux file systems.

Yet another method could be to import both folder into a new library in calibre and use calibre to find, examine and handle duplicates.