I did that today, cleaned up everything, unfortunately it didn't solve the problem.
This is how it looks like now:
View attachment 476448
I will try reading the resistor values next to the left joy con's handshake IC next, my multimeter broke down for some reason, so as soon as I get a new one I will post whether there is anything out of place. From just looking at them I have no idea why they wouldn't work though.
View attachment 476449
Thank you, I found that thread earlier and already cut off the shield on another side to see whether any traces were damaged before, but they all look fine to me (except for the trace I posted earlier, I don't know whether it has anything to do with the joy cons though and it looks to me like only the mask came off and the trace is still intact.
View attachment 476450View attachment 476451View attachment 476452View attachment 476453
I'd be glad for more tips and ideas on how to further debug this. If the IC resistor values are fine I will probably test continuity from the rail to the connector next, but I really don't know why that would be a problem as I didn't touch any of those parts.
Thanks again for all the advice!