You stated yours as a config issue, mine is probably a controller issue. Since i’ve always sort of had issues with the xbox 360 rock candy controller. Over time it randomly switches from generic xbox controller to harmonix controller. When it did that it stopped working all together.
I also did this
removed all retroarch related config, reinstalled retroarch from binaries. remapped controller using the retropie-setup script.
Did not fix my issue.
Also when ES does the config input R2 and sometimes Thumb Left never registers and gets skipped.