I have been effected by this bug for a long time.   In the end, I
resorted to using dropbox, which works reasonably well (with no web
access or course).  Recently, dropbox access has been blocked at work,
prompting me to look at this again.

I tried most of the things mentioned above, to no avail.  Then I read
some other bug reports with complaints about conflicts in templates
(templates do not show up in note lists, so cannot be deleted manually.

So, I deleted these manually with the following procedure

quit tomboy

Romove all notes from web server.  I found the easiest way to do this
was to sync an empty tomboy instance to the web.

Move old tomboy notes to backup:
mv  ~/.local/share/tomboy ~/.local/share/tomboy.bak

Restart tomboy, which will create a new library.
Delete all notes (start here etc)
Set up sync to ubuntu one web account and sync. 
Check online at ubuntu one to see that all notes are gone.  
quit tomboy

Then, clean out all old template notes from backup library

cd ~/.local/share/tomboy.bak

locate old template notes, those that have been renamed in previous sync
attempts.

grep "Template (old)" *

remove the offending notes (rm ...)

Move library back to where tomboy expects it

rm -fr ~/.local/share/tomboy
cp ~/.local/share/tomboy.bak ~/.local/share/tomboy

restart tomboy, and sync to ubuntu one.

This seems to have fixed my system now, and I have 419 notes synced to
the web.

Hope this helps

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https://bugs.launchpad.net/bugs/575937

Title:
  Can't synchronize Tomboy Notes: Server returned 404 NOT FOUND

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