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I have not had any problems with it personally, but I also have not tried reverting to a time-machine-generated back-up of OmniFocus. I'm gonna ask around and maybe do a little testing to find out what the deal is.

My current (slightly paranoid) suggestion would be to exclude the active database from Time Machine backups, but make sure to include your Focus backups in the Time Machine backups. Not so much because Time Machine might scramble the live version of the data, but because Time Machine might make a copy of the file when Focus is sort of in the middle of writing something, so if you tried to restore from that backup, it would just give you errors, instead of your data.