I’ve reinstalled many times and never lost my controller settings.
Also I’ve run into the same situation with the sim reinstalling itself when leaving the beta, but never more than twice. During the SU1 beta I was switching between the beta and the production build for various reasons.
FS2024 is running the same for me as before this mess but FS2020 seems to be having performance and stuttering issues. Have you had a chance to try it yet since you reinstalled?