If I remember correctly, restoring from backup also clears out the various client files in the sync database, so the database compacts down to one transaction file.
Explanation:
Your database has one action. You add actions B and C. You change action A, and then delete it. While you're syncing, your database would look like this:
<Start with A>
<add B>
<add C>
<change A>
<delete A>
After you revert, instead of storing each step, we compact everything and just store the end state. Smaller and less work, but as you saw, puts you in the position of picking one or the other database to win out. You can't merge transactions from various sources any more.