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Santra, are you able to access your iDisk contents when you are not connected to the network? If so, you have a local copy of your iDisk on your machine (in the form of a big disk image) which is synced with the data on Apple's servers periodically. OmniFocus communicates directly with the servers to make its changes, so if you tinker around with the file and then OmniFocus tinkers around with the file, it's possible that the copy you worked on will overwrite the copy that OmniFocus made the next time your Mac synchronizes its copy of the iDisk. An easy way to check if you have iDisk sync turned on is to just look at the .Mac/MobileMe preference pane in System Preferences. Click on the iDisk tab and it will tell you the status of the iDisk and whether you've got syncing turned on.

To answer your other question, MobileMe sync works just fine with multiple Macs. It's a supported configuration. I think Andrew is saying you wouldn't want to tinker with the database from the Finder on more than one machine for much the same reason that he's nervous about tinkering with the database in the Finder if you have a locally synced iDisk.