@g0nz0uk it could be that the driver support has changed in the kernel for this controller, and it's seen differently.
can you not just reset your controller configuration in emulationstation, and rebind? -
Choose Manage Packages.
Choose Manage Core Packages.
Choose emulationstation (Installed)
Choose Configurations / Options (it may also be named Configurations Tools)
Choose the option to Clear/Reset Emulation Station input configuration.
Choose Yes to proceed to clear the controller settings.
Then when you return to ES you will be asked to rebind your controller, that will then filter through to all cores, etc.