You could also manage books on your computer, and sync it up to the server, but finish by running
Code:
calibredb restore_database --really-do-it
to have calibre rebuild the database and fix all errors of that nature.
Or export "cleaned" books, with their proper metadata, and import the cleaned copy on the server via the CLI.
Or get Ubuntu on that laptop.
Aside: my favorite way of transferring data to another computer is the old-fashioned way, via rsync.
Heck, there are GUIs for rsync.