Drop Shipment Entry "Shipped/Received" unchecks after AR invoice created

We have large volumes of drop shipment orders that come from EDI, and have a BPM written so that when the vendor sends back the ASN after they’ve received our PO, a drop shipment entry for that PO/Order is automatically created and it is automatically marked as “shipped/received.” We have the “generate shipment invoices” process running on a nightly schedule, so the AR invoices are automatically created the same day. The problem is that after the AR invoice is generated, the drop shipment entry “shipped/received” Boolean field is unchecked and greyed out. This makes it impossible to generate the AP invoice, because those lines are no longer considered received. Because of the volume of these orders, we want the drop shipment process for this customer to be completely automated. We do have drop shipments for other customers that are not automated, and we do not experience this issue in those cases.