Comment 22 for bug 845321

What I sometimes experience if I try to sync after tomboy has lost track
of what really happens is that tomboy doesn't dare to touch the contents
of notes on the local computer or on the server and finds it less risky to
 - rename all notes on the local computer it doesn't dare to replace
 - download all notes from the server
 - and afterwards to upload all notes it has renamed.
The advantage of this approach is that you are sure not to loose a thing
The disadvantage is that you might end up with loads of notes in two
versions: An old and a new one.

Not sure if you encountered this kind of behavior.