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If you've made data entries in both before establishing the link between them, OmniFocus has no way to decide how to merge them. If you've got a significant number of changes on each device that you don't wish to re-enter, the easiest thing to do is probably to use File->Back Up Database on the desktop version to save a copy of its database. Then sync the iPod, and tell it to keep the iPod's database. Next, sync the desktop, and tell it to keep the sync database (which contains the iPod's data). Now you've got the iPod's data on both. With OmniFocus already open, double-click on the backup file you made, and copy over any projects and actions by dragging them from the backup file's window to the other. Subsequent syncs should not produce the message you saw.