No problems man - from what I've been reading.
You want to cut your pepper down, above the new growth line. So above where new leaves or stems will off shoot to give it the best chance of survival. You'll be cutting some roots around the plant, and underneath, but that's ok. Take er inside - nourish it and you should see new growth. Keep it pruned and short, then next year when you plant it out you'll be ahead of the game. Look up 'Bonsai pepper plant' and 'fatelli' He has a great guide on making your pepper plants into bonsai trees, but the method is also used for overwintering - PLUS - you'll get the bonus of some production over the winter if you do it right.
Ah hell - here!
http://www.fatalii.net/growing/index.php?option=com_content&task=view&id=95&Itemid=105
I spelt it wrong and took awhile to find it myself right now. ha!
Keep us posted!