[whpalmer4]

The sync code is designed to allow you to make changes to a common starting point. It sounds like you synced two different databases, which causes OmniFocus to ask whether to keep device or sync database—but in either case, one is replaced by the other. What you need to do is merge them, and probably the best thing to do is to contact the Omni support ninjas on Monday by phone and have them talk you through the process. It isn't particularly difficult, but it needs to be done correctly or you could lose data.