I also bought a GoDaddy Online File Folder just for this. I tried several times and got the flat file message as well. I finally did a sync with a local external hard drive, then copied those files to my Online File Folder and directed OmniFocus to sync there.

It has worked for a few days at a time, syncing my iPhone to it as well. Then eventually I get an error message and it stops. The most recent message told me the database had been reverted to an earlier version and could no longer sync.