in my opinion the best way is:
case 1. delete the transport order with se10 (if you don’t just released them, otherweise delete the order in STMS), undo the changes in customizing and delete also the new transport
case 2. undo the changes in customizing, transport in QA and delete both transport orders in STMS
Very important is that the 3 systems are aligned, so be sure to make the right step back in configuration.
I hope that can help.