[Tim Wood]

In your ~/Library/Application Support/OmniFocus/OmniFocus.ofocus file, there should be a bunch of .xml files. Is there only one? There should be one per transaction unless you've used the 'Rebuild' menu option to compact the file.

OmniFocus should never re-write or modify these files; only adds new ones, unless Rebuild is used. In fact, you can't even backup over an existing file right now due to paranoia about losing data.

If you are in 10.5; do the Time Machine backups show any data (what OS you are on would be useful info either way)? Are there any messages in /Applications/Utilities/Console.app from OmniFocus?

Are you using any sort of file synchronization software or a network home directory? Not that I can see how that would explain undo disappearing stuff, but just asking in the interest of collecting data.

Our data loss rate has been within epsilon of zero so far and I'd like to keep it that way, so I'm eager to get to the bottom of this and either improve the UI or fix the app if it truly is a data loss.