This is a bug that some people are reporting with the iPhone. It is not supposed to wipe your application data when it installs an update, but sometimes it does. We don't know why or if there is any pattern to when it happens, and it's not limited to OmniFocus - it appears it can happen with any application that saves data on the phone. (It's possible that the bug was fixed in the iPhone OS 2.0.1 upgrade, but we don't really have any idea. Do you have 2.0.1 installed?)
If you have a recent backup of your iPhone/iPod touch in iTunes, you can restore that backup to get whatever data was on your phone at that time. THIS WILL WIPE OUT ALL NEWER DATA ON YOUR PHONE, including any upgraded applications, so if your backup is not recent, it may not be worth restoring from it. If you _do_ restore, you'll need to reinstall any upgrades that you installed after the backup, including OmniFocus, and there is no guarantee that it won't lose your data again when you do that, as we don't know what causes it. (However, if you restore and then set up syncing to get your data backed up to MobileMe or other WebDAV server, then if the upgrade loses your data you can just reconfigure syncing to download the data.)
To restore from a backup, connect your device to your computer, then right-click on it when it shows up in the source list in iTunes and choose the restore option.
I hope that's helpful, and I'm sorry that I don't have better news for you.