I do see your point - my over wintered ones (all outside since May) have all produced red fruit unlike 90% of the others, even those in the GH. But try starting indoors in Feb next year. You'll need heat to germinate them.
Afraid I don't know whether a chilli puts up with that sort of root disturbance. I imagine it's best done when the plant is as dormant as possible. If no other advice is forthcoming my best guess would be to transplant, trim the roots and immediately cut back to a stem of 6" to 12", at least clear of the woody part of the stem.
It looks like a cherry bomb: I've over wintered Ciliega Piccante/Satan's Kiss which is an Italian 'cherry'. I cut it back round about September and it looked great at Christmas - little red balls, very seasonal.
As Georgie said, chilli nuts tend to be manic seed collectors. You can only grow so many plants and I have spare seeds of the Ciliega and other varieties I'd be happy to send to you rather than let them go to waste. PM me if you're interested.