@mitu Thanks for the link. I checked it out, but it doesn't appear to fix the main problem of disrupting retropie. It only fixes games with mic issues, if I understand it correctly.
This was the issue I was having: https://retropie.org.uk/forum/topic/10110/drastic-nds-emulator-breaks-run-command-emulator-configuration-prompt-in-retropie4-2/30
Though in my case, it seems to have disabled the retropie setup menu as well... even after I uninstalled it. I switched to my backup SD card and so far no problems with the retropie setup menu, although, I still can't get other systems to boot after I've launched a NDS game.