No. It calls input configuration.sh anytime controllers are configured in emulationstation. there should be a es_input.cfg.bak file that may still have it, if not when I have access to my pi later I’ll post my config. Also just out of curiosity did you start from a fresh image or did you upgrade from a previous version? That may also explain some of the inconsistencies
you’ve been having if you upgraded.
(Though if you followed my video I show how to build the retroarch autoconfig file manually which accomplishes the same thing the script does)