Tomboy notes are now stored in ~/.local/share/tomboy, and have been since Tomboy 1.0 (which was shipped in Karmic).
If you still have notes in ~/.tomboy, they are from Tomboy 0.14.x (Jaunty).
I'm not aware of any Tomboy dataloss bugs that would cause you to lose notes like this. On the off-chance that you accidentally deleted them using Tomboy's UI, you might want to check in ~/.local/share/tomboy/Backup.
Tomboy notes are now stored in ~/.local/ share/tomboy, and have been since Tomboy 1.0 (which was shipped in Karmic).
If you still have notes in ~/.tomboy, they are from Tomboy 0.14.x (Jaunty).
I'm not aware of any Tomboy dataloss bugs that would cause you to lose notes like this. On the off-chance that you accidentally deleted them using Tomboy's UI, you might want to check in ~/.local/ share/tomboy/ Backup.