@lostless i couldn’t swap them in the RetroArch menu because the confirm and cancel buttons on the controller wouldn’t work in RetroArch for some reason. So here is what I did and it worked perfectly. I downloaded retropie version 4.2 and re flashed the mini sd card. Now it works just fine. But thank you for your suggestions. Love this community.

@meleu the "Hack on" was the issue, but i noticed it didnt well with it off. the problem i found was that the Firmware update didnt go through on the controller, once i was finally able to get it updated and reset it up following the step by step guide you linked i was able to get it working perfectly and connecting every time. Thanks for your help in my small matter.

@simonster Thanks for the reply. Unfortunately for me, I'm using the Pi Zero. I haven't tried a lot of GBA games yet, but lr-gbSP is much better at playing games on the Zero than lr-mgba is.