Can't tell from the pictures, but I see that quite a few of the dead limbs are apparently coming from nodes next to where you chopped the trunk pretty hard.

Look at the cut ends of the trunk. Do you see any kind of white fuzziness in the cuts? Has the center of the trunk receded, leaving a kind of hollow straw like appearance?

These are signs of a fungal infection that will kill your peppers very quickly. If you see signs of it, your only recourse is to chop the plant back hard. You have to get below the infection, and then sterilize the chop with peroxide. Repeat the peroxide spray every day or two for at least a week.

If the fuzz reaches the main trunk of the plant, its pretty much game over.

The light green could be nutrient deficiency. If it's the same pot for 2-3 years, just make sure you give adequate fertilizer or even repot once the plant is not stressed and losing its leaves.

If it is actually the same pots, I could see how after 2-3 years, it might be root-bound in that size pot, also, especially since we don't know how large they were able to grow to before you pruned them back down to that size.

One more thing, did you spray them with a overly potent concoction recently? (fungicides etc) If so then it's the newest and most sensitive foliage that would be affected first. This can also happen if someone sprayed too much lysol or cleaning agents in the room recently. Plants tend to bounce back from these setbacks after the initial die-off.

But more importantly, make sure that it isn't an infection as outlined by Edymnion above.

The peppers just overwintered in the pots and are going back in the ground this weekend. Nothing sprayed on the leaves or cleaning sprayed in the room. The center of the trunks has receded and turned a yellowish color so I took Edymnion"s suggestion and cut trunks back half with disinfected clippers and sprayed with hydrogen peroxide.

Thanks for all the advice. Fingers crossed that they survive.

Update - Both peppers have died after planting in garden. :(