I'm assuming you probably did a LON download? It is accessed through menu 5-7-1. You wouldn't think the software versions would change just from getting the ADON repaired but you never know. I would try a LON download (5-7-1 and when it finishes its sequence reset the controller) and then do an ADON learn again. I believe 0026 is a drive fault but I don't have the codes in front of me. Was it faulting on 0026 before you reversed phasing? Also wouldn't hurt to verify the correct encoder and resolver connections.

Edit: Check if there is a parameter to reverse motor encoder feedback signal. If there is reverse it and see if that gets you anywhere.