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I'm a little suspicious of the exact details (do you have repeating actions in your Inbox?) but I agree that the conflict resolution is the likely culprit here. I think it should be possible for Omni to provide an instrumented image that could leave a slime trail that will confirm that what we suspect is happening is really what is happening, though my expectation is that they probably won't be eager to do that.

Have you ever observed this issue anywhere other than the Inbox? Is the Inbox on the desktop completely empty when you see this? How long has it typically been since the out-of-sync device has been synced? When you add something to the Inbox on the out-of-sync device, does it have a context set? What are your settings for sweeping items out of the Inbox? What's the simplest test case (ideally, including a timeline) you can set up to reproduce the failure? I do the very things you describe all the time, and never have any of the problems you mention. Any of the support ninjas can attest to my ability to torture their software, too :-)

You can improve the odds in your favor, however; whenever you do a bunch of work on one device, sync it, then sync the others! Think of it as backing up your data; if the change is worth making, it's worth backing it up. As an added benefit, you'll keep the uncompressed portion of your database small, so syncs will tend to go faster.