I just got hit by this. Using Calibre on 2 Ubuntu systems with Dropbox. One is my main system, the other one is my wife's which I occasionally borrow. I did a number of edits on the main system, then went and started up Calibre on the second system - I don't really recall if I saved anything or not, or if I shutdown Calibre on the main system (it tends to stay running for the content server and because there's no reason to stop it).
Anyway, when looking at Calibre on the main system I noticed it lost most of my changes from yesterday. At first I decided to just recreate the updates, but then remembered its Dropbox - and it had a copy of the main systems' metadata.db file. I put that back in place and got all my updates back. My fault for using it this way as I know Calibre isn't meant to be used like this, but good to have the backups
So it might be good to have a 'start Calibre in read-only mode' option. I could setup an rsync pull, but as was said above, Dropbox just works (though a cron job is pretty trivial). With the option, I could even start it up with write enabled to do some edits on the second system if needed, but that's probably going to lead to problems again
Maybe I'll look at VNC and rsync again...