I'm wondering why you couldn't do a bit of root pruning in a deep water container to encourage a more vigorous root mass. Also, to keep nutrient at a higher level. Any thoughts?
You can prune chiles pretty much as you want, it's hard to kill a chile.
Â
This is a tepin I pruned, put it back in aeroponics and had fruit soon.
 tepin1 by Willard Bridgham, on Flickr
Â
Yeah it doesnt seem to be a problem, I chop out huge solid sections of roots in my out door hydro set up to
make more room for new roots and water flow.