I have now something similar. When I sync my notes, al my 140 notes get
removed.

So I delete  ~/.config/tomboy/manifest.xml
I copy my note backups to ~/.local/share/tomboy
I sync, and all 140 notes are uploaded to server (Ubuntu One).
I sync a 2nd time, and all notes are removed locally again.

I followed this guide to purge the server: 
https://one.ubuntu.com/help/faq/how-can-i-delete-all-my-tomboy-notes-from-the-server/
But I still have the same behavior. Every computer I power on gets all my notes 
removed. I restore backup to ~/.local/share/tomboy, all notes uploaded again 
and removed again on 2nd sync.

The part about purging your couchdb locally doesn't work as the linked
script is not available anymore. Is that still relevant, or for older
tomboy versions?

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https://bugs.launchpad.net/bugs/580333

Title:
  tomboy notes disappeared

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