The contact ring inside the dome should be conductive, and when pressed, should bridge the two contacts.
Things to watch out for with the pen: 1: don't bridge the traces, and 2: don't get too close to the key contacts.
I use a pink pearl eraser to clean the contacts -- cleaning the traces shouldn't be needed unless there's a fracture, in which case you clean first (99% IPA), dry, and THEN use the pen over the area to ensure any breaks are bridged.
The goal is to have lowest resistance possible from the contact end of the trace to the far end, and to have the contact ring being the ONLY thing bridging the contact to the trace.