@cberwaldt , @greggchopper , here’s an official reply from Acumatica. This might save time for you and for others who stumble across this thread:
Issue: When Amazon sales orders were prepared automatically in Incremental mode, some merchant-fulfilled orders were not retrieved and did not appear on the Process Data (BC503000) or Sync History (BC301000) forms. This issue could occur because the incremental preparation process advanced the synchronization boundary beyond the time range actually processed by the Amazon Orders API. As a result, orders whose status changed from Pending to Unshipped during the skipped interval could be permanently omitted from synchronization.
Workaround: Configure the sales order preparation process to use Incremental by Date mode with @Today-1 in the Prepare After box and @Today in the Prepare Before box, or run the preparation process in Full mode. Missing orders can also be imported manually by using the Add New action on the Sync History (BC301000) form.