So I'm wondering if it's safe to use the header since one GND broke off the first time I tried to plug it in.

Pic of USB 3.1 header pins

Third row, second pin is the one.

The header is connected to two USB sockets, can I figure out with a multimeter which USB port that belongs to (if any) and just not use that one?

Edit: found it, on one of the USB slots the first pin (GND) has no connection to the metal cover (also GND) while on the other there is connection.

  • This could be repaired by a competent solderer. – Keltari Nov 6 '18 at 23:25

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