One post I've read mentioned that to replace a fliptronics 1 board with a fliptronics 2 board, you may need to replace the flipper leaf switches with opto boards.
TAFG does use opto boards for the flippers along with a fliptronics 2 board, so it does lend some credence to the theory.
I have not seen any details on what wiring changes that might need to be made. You would need to run additional wiring for the opto board electronics, at least.