@tamperedmedia i think I fixed it . Double checked all of my wires and ,while identical, select and start weren't connected in the right spots on the encoder. Once wired correctly I set both bindings in retroarch without bothering to set player 2 on the retro pie home screen. It still inverts up and down for player 2 on the main menu but it seems to work properly in game so it'll work as it is.
Hopefully it won't break again, appreciate the help.