When the amp is set up for three-wire operation, the polarity switch has no purpose. Just remove the cap, and live with the useless switch.
Of course, there are other things one could do with it. On my 200S, I wired it to remove the feedback loop. However, I don't find that to be a useful mod, so I'm going to remove it. Greg (SoundmasterG) used his as a ground lift switch. Useful, in some situations, but a lot of work to make it happen.