Thank you eschwartz for pointing that out.
Not being familiar with FreeFileSync, I wonder if I could synchronize the other way - keeping my linux version of the library as the master, and bringing updates to my laptop to get rid of any case sensitivity issues?
That would mean that any editing of the library would have to be done on the server, which is a bit awkward. Any ebooks downloaded to the laptop via the Kobo software (or Amazon, etc) might also be an issue. They'd need to be added on the server library rather than the local laptop copy.
Perhaps I should be looking at running some sort of graphical access to the server using X, so that I could run the server version of calibre remotely on the laptop and get rid of the laptop copy of everything? Still would have to figure out the best way to get purchased Kobo / Amazon books onto the server. And it would limit my ability to load books onto the Kobo to wifi only without the local copy of the library and access via usb.
I understand the limitation around not accessing a library via a networked drive. It's definitely an unfortunately limitation in my situation. It would certainly simplify things!