Sounds like your problem is on the output side of the RS485 chip. Possibly shorted to ground. High impedance path to ground created by the lightning. That should be visible, I would think. My other thought is that the RE enable pin on that chip may have a problem. I think that would prevent the chip from outputting to the PIC. Not sure how RJ did this on the board. He could better speak to that.
Maybe you can post a good pictures of the board front and back. That has helped before identify issues. It has to be good enough so that we can zoom in and look at traces.