Clovercon-Controller not configured

[/classicSNESmini]

Sooo i ran into a problem. I wanted to manually reconfigure the snes controller on the n64 core to map the analog stick to the buttons.
It worked and i played Majoras Mask on the snes mini! But then when i resetted and restarted the controller stopped working in all games, even n64.
It works in the snes menu, but when i enter ANY core, it states in the corner "Controller Clovercon Patched/Remapped to core" and the game starts. I can't open retroarch menu with the buttons i set or not even with the default commands.
I was able to open the OptionsMenuMod and as advised on some threads i deleted the core overrides and reset retroarch via OptionsMenu.
That did not help, so i went FTP onto the snes and deleted retroarch.cfg and retroarch_core_config.cfg in the libretro menu.
Now i am in a mess... nintendo menu loads, anything past that it now states "Clovercon Controller #1 not configured (0/0)".
That is it. Reinstalling Retroarch does not help.
What now? General reset? Repatching the core? I wonder why the controller now stopped working and also the system shows it is not configured. So actually the reddit thread advice made it worse...
Maybe i can use the config in the hakchi folder? This was not changed as i did it all on console...

submitted by /u/Bitter-Surround2460
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