From what I can tell and reading the different manauls for my 08 heritage the circuit board acts as a junction block making it easier to plug all the different connectors to and serves no other purpose. I found the following statement in the service Manual.
"The FLST, FLSTC, and FLSTF Softail models are equipped with a tail light assembly that uses a mini harness and circuit board to simplify replacement."
If you are doing away with the stock fenders and lights you should have no need for the circuit board as you will not be using the factory connectors either.
I am not saying postively 100 percent that it serves no other purpose, what I am saying is I can find nothing in the manuals that says it does. If it where me I would check the operation of the new lights without the circuit board in place before doing a final hookup of the new lights and wiring, keeping the circuit board handy if needed but I doubt you will.