Never seen such problem. I went from UC300USB to UC300ETH also, but I have changed the whole thing, not just the CPU (FPGA) board.
No, that is not going to solve it. If you have connection with the board then the communication works and using direct cables won't do any good to solve your problem.
I don't think so, but it is not impossible, though highly unlikely. I think if I were you, I'd replace both cards, not just the main board with the FPGA.