Hey Roggie-
When you click sync on the desktop, I can confidently say that you'll be asked to choose Local or Server copy. (You would want to choose Server.)
Data is still backed up if you choose Local, though.
To be safe, I might even make a copy of the OmniFocus.ofocus folder on your iDisk.
Hope that helps, but if you want, write in to
omnifocus@omnigroup.com .