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If you open up OmniFocus' Sync preferences on all your devices, and none of them have the "MobileMe" sync type active, or a MobileMe address entered in the "Advanced" tab, then OmniFocus isn't using your iDisk to sync.

Since this is still happening, though, I'd open System Preferences on your Mac, open up the MobileMe pane, and then click into the iDisk tab. If the 'iDisk Sync' option is enabled on any of your Macs, that's likely what's causing the messages you're seeing.

With that option enabled, your Macs each keep their own copy of the contents of your iDisk on their hard drives. The intent here is that you can work with the files on your iDisk even if you don't have a network available; any changes you make will be synced back to Apple the next time you've got an internet connection.

Deleting a file from the iDisk servers removes the copy on Apple's end, but doesn't immediately remove those additional copies on your Macs. In the ideal case, the next MobileMe sync on each of your Macs sees that you deleted the OmniFocus file from the iDisk server, then turns around and does the same on each of your Macs.

That doesn't always happen, though; if MobileMe sync gets confused, it'll instead see that the file exists on one of your Macs, doesn't exist on the server, and resolve that by trying to copy the file back up to the iDisk server.

If more than one Mac gets confused in the same way, you could end up in a situation where different versions of that file are being uploaded to the iDisk server, producing the 'changed on both sides' error message you're seeing.

I'd suggest using MobileMe preferences to temporarily turn off iDisk sync on all your Macs, and then delete any OmniFocus databases you find on the iDisk. At that point, you should be able to turn iDisk sync back on in System Preferences.

(At no point in this process do you need to mess with OmniFocus' sync settings; leave your devices set to sync with our server.)

Does that help at all?

Last edited by Brian; 2011-04-06 at 11:54 AM.. Reason: 'temporaril' -> 'temporarily'. I hate typos.