The last dozen times or so that I’ve tried to sync my Omnifocus mobile, it’s presented me with a message that my mobile database is incompatible with the sync database. It offers the choice of keeping the version that’s on the device or keeping the sync version. I always opt for the sync version, but then it takes forever to sync.
I sync with Omni Sync Server. The desktop OmniFocus is 2.04. The mobile version is 2.4.
I’ve seen this happen a long time ago for me. I think if you haven’t synced a device for a long time, there will be considerable changes between the database on your mobile device and the database in the cloud. It might be checking for a time stamp or something. If OmniFocus is detecting that there is a drastically different version, it will ask if you want to use the database on your mobile device or the cloud version. How long has it been since you synced all of your devices?
The last sync that succeeded was about a week ago.
Another relevant thing, strange as it seems, is that the location of the device seems to matter. When I try it in the office, with the device and the laptop on the same wifi network, OmniFocus on the device never asks whether to keep the local database or the sync version (but the sync works intermittently). But at home, it does ask that.