I've never worked with a PCB before, but when I was building my keyboard which has a hand wired matrix, a few keys wouldn't register/be always registered on aquakeytest and all I had to do was resolder the switches and it would work fine. Assuming the switches were perfectly functional beforehand (i.e. it's not a debouncing issue) then I would try just resoldering the switch onto the PCB, but if you didn't test the keyboard prior to de-soldering I would resolder a newer switch instead as it might be due to a faulty switch.