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Are you sure the iPod touch is syncing? I would use the Show Clients button in the Sync portion of the OmniFocus (desktop) preferences to see when the desktops think the iPod touch last checked in. Then press the sync button on the iPod touch and make sure it completes (no "!" in the middle of the icon) and check the Show Clients display again (you'll have to close it and reopen it, as it does not refresh). If the line for the iPod touch doesn't change after doing that, then either it isn't set up for syncing or is syncing to a different location than the desktops.

To be on the somewhat safer side, I would plug the iPod into the computer where it interacts with iTunes to make sure you have a recent backup. Be sure while trying to figure out what is going on that you always answer "local copy" to the question of "local copy" or "server copy" when doing a sync on the iPod.