I already found a fix. Pull the battery out of the switch and hold the power button for 15 seconds. Re-insert battery and start as normal. I'm currently attempting to find a software method.
EDIT: I've not yet been able to replicate the battery bug myself yet which is proving to be harder than I initially expected it to be. I'll see if I can force my switch to die on Linux overnight and test from there.
Just followed your steps and now the Switch reads the battery percentage correctly, awesome. Thanks!