I suppose you have a basic multimeter handy? One option is to use the board / image / schematics in Github to check where the on the RPi header that particular encoder is hooked to, and use a multimeter to trace back from there.
(I suppose the initial brute force option is to first reflow the whole RPi header and see if that fixes the issue, as it might be a connection issue between the shield and RPi. But if that doesnāt work, I suppose itād be best to check where the signals from that encoder should go to, and measure whether they are actually connected to where they should be)