I would check the hot pepper forum.

I did the same with one plant but it's now planted outside and has about a hundred peppers. I would leave it alone and not prune until it's ready to be planted outside. Keep in mind I'm in Florida but the same should be true for you when it warms up where you are. Some Epsom salts at plant-out time will help a lot,

Harden it off and plant it back outside when you think it's safe from frost. You have a head start - congratulations!

I overwinter peppers routinely. Here in central Texas, it's just a matter of covering them outside. Don't have to bring them inside. (Well, except for a very rare very hard freeze.) But peppers are, for real, perennials. As noted, you have a big head start. I get my first fruit of the spring season in April, and actually get a few stragglers before that.

Just leave it as it is until you plant it outside and then prune any dead limbs on it. I have a birdseye pepper plant that I have been growing for about 10 years and I never do anything to it other than trim it back everyonce in awhile when it gets too big. It will freeze back to the ground some years but it comes back and grows fine. Right now the plant is taller than I am.