To get around this, I have backups take place each night, then applescripts set on on cronjobs that shut down server, upon up the back ups in FM Pro and make sure everything comes up okay by running test FM scripts. Once these pass, then FM PRo is closed and the backups are copied to another drive. From there, the old hosted files are corrupt because closing the server damages them. So, then another applescript triggers and copies the back-ed up databases over the damaged ones and Server is re-opened. Ah, but remember to make sure the back-up actually happened before shutting down server(which doesn't always happen) lest you be left with a bunch of damaged files that need to be recovered in the morning.
All of these tasks and applescripts have taken weeks if not months of development and debug. A completely un-reasonable thing to have to do to work around FM Server 5.5. It all finally works, but it was a painstaking iterative process, as different things start failing along the way.