After an incident with an untrained powerboat helm I am now minus one pole, P&B inform that the new poles have the pole up haul slightly further back than older designs.
Will this make much difference and if so is it easy to alter the older pole to match without weakening it too much?

One pole will fly a couple of mm higher than the other would be the only difference. I doubt you'll notice it. If you do alter the other pole make sure the screw has some reinforcement (Epoxy filler) to screw into or it may not last.