I've overwintered multiple hot pepper types. I usually cut them back so there are few branches with several leaves per branch. I picked all the peppers off, dug them up and put them into a 5gal bucket. Then I brought them inside and put them in a room full of windows. I watered them sparingly, trying to keep the leaves on them from falling off, but mainly to keep them alive. Several pepper plants I kept over 4 years. I think a trinidad scorpion and a ghost chillie were among the longest I kept alive. When the ground warmed up and the threat of frost was over, I brought them outside to grow. At one house, I kept them in the 5gal buckets, but drilled holes in the bottom, so they would drain. At my newer home, I started removing them from the buckets and planting them into the soil. I felt planting them in the ground was better as it allowed the roots to grow out and the plants seemed to produce better. I never noticed any difference in heat or quality of the peppers, just that I got more of them each year and they fruited earlier. Sometimes here in Virginia, I got 2 crops of peppers from the same plant. I think as long as you can keep them alive over the winter they will thrive once planted again.
The only fertilizer I ever used, was the compost I made from lawn clippings from my backyard, so not sure why your flavor changed, but it could be due to over fertilization.
