On peppers i am not a pro, but i have grown other mother plants for cloning which i am sure i pruned more then you have. I have never experienced this. I am starting peppers for my first time this year (well hardcore peppers ive grown jalapenos, anahiems, and wax peppers). So i am still very new to pepper growth. Have you checked your soils ph levels and such? I would even try a groth hormone or maybe some b1 to reduce any shock to the recent changes in growing conditions. But i am no expert, please only read this as my experience and not facts. Hope some of this can help!
"b"

Thanks for the response "b". I think you are right about the pruning not being the problem. I haven't tested the soil, but they are in the same 5-gallon container they have always been in. I think I'll just transplant them into the garden and hope they recover.

They are probably root bound. They may need some root pruning.

Root Bound! That sounds right. I don't generally grow in containers so hadn't thought of that. Thanks!

Top-pruning and root-pruning have helped my peppers survive through the winter.
I also overwinter my plants in smaller containers - .7 gallon is what the label says.
The smaller containers are easier to keep warm, and they hold less soil-volume.
They dry sooner - which is a plus during the cold, lightless days of winter.

Josh