Hey man,
I was also so interested in this as when winter comes here is Swiss land it's really cold and nothing but pine trees will survive outside, so what to to? Chop em.
Did you also have to cut the roots right back? How much did you leave on? I'm very keen to have a little chillie tree in my house. What a conversation piece.
I had the same problem with my hydro, no space, too crowded, some plants growing faster than others stealing the light, all these things, so I had to plant some of mine into pots on the window sill.
Please keep us updated on how it goes, like when the poor thing gets some foliage back.
Keep well