I fixed this by doing this:

Adding some random text to these two notes

egewg

I shutdown Tomboy.

Then going to ~/.local/share/tomboy in a terminal.

grep egewg *

Then I got two filenames. I moved these two into the Backups directory.

Then re-started Tomboy and the notes were gone.

-- 
Tomboy shows templates as notes
https://bugs.launchpad.net/bugs/664963
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