Indeed you linked the PR we discussed about. It will be merged in soon meaning I'll be able to proceed with testing of Staging's upcoming release. It should be going fine yet count on me to report anything should I hit another roadblock.
As usual thanks a lot for your assistance and always swift replies. Truly appreciated.
Upgrading the OS is not supported by Raspbian nor RetroPie. You probably have found some instructions on how to upgrade using apt and updating its configuration files in /etc/apt, but it's not a recommended process, especially for a beginner.
EDIT3 (and the last): NEVER and NEVER run an emulator using sudo command, that's why I could not properly configurate my controller - Retropie runs emulators without sudo I suppose...
Ah yes, this might make some sense after all. If you ran it with sudo the first time, the configuration file probably got saved with root ownership or permissions. Then when it runs as the regular pi user from ES, it doesn't have ownership or permission to edit the file most likely. I've seen the Windows version of this snafu before.
/home/pi/RetroPie (ROMs, BIOS files, splash screens)
/opt/retropie/configs (configs for RetroArch, EmulationStation, also your scraped game library)
/etc/emulationstation(custom themes as well as the systems ES has access to)
The RetroPie documentation has info on how to copy files. WinSCP or Filezilla are probably the easiest programs to use.
Copy those over from the 3B to the 4, and you should be fine. Note: after you flash the image onto your RPi4, you'll need to boot up with it for RetroPie to finish installing, then you can turn it off and start copying.
If you want to set up a new model, simply clone your /home/pi/RetroPie folder to your PC, install RetroPie on the new SD card, delete the new /home/pi/RetroPie folder, replacing it with the existing one.