First of all thank you very much for your reply
Already did that, the issue still happens without the joycon attached.
On the switch those are fine fortunately. I'm not using the joycon where I messed up the pins anymore but those weren't fine at all so they might very well have caused the issue.
I tried that too with the same unfortunate result. It appears that the battery is really at fault and I ordered an replacement (The warranty on my switch is over already so I have nothing to loose).
I'll report back once my replacement arrives.
Yes please report us!
I think linux is fault.
Maybe you can fix the problem in linux itself?
can I load or re-calibrate the battery on Linux ?