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Could you please check in an older version, say 2.0.5 or 2.1, from our downloads page if the Notes in your Backups are still there to see if it's maybe a problem with Ulysses 2.1.1?
We have seen rare issues with dropbox and similar sync services. I have had it once with my projects. We did not yet find out any details and it seems to appear rather random. Ulysses may at times change a few hundred files and folder, and I could imaging Dropbox getting confused from time to time.
Anyways, that's why it's good to have a backup outside of dropbox, like Ulysses does them :)
This is weird, indeed. Is there something being printed to the Console? You can find the "Console.app" the easiest by using Spotlight. The select "All messages" on the left and maybe filter for "Ulysses" in the upper right.