The footprint library table (The thing that holds the information of what footprint libs are loaded) is not overwritten on kicad update.
You can conform that by looking into pcb_new->preferences->footprint library manager.
It will still hold entries that start with KIGITHUB (or have plugin type github)
You would need to do that by hand. An explanation for that is: How can i install a specific version of the footprint library?