So I bought a Carolina Reaper plant in the fall, it had been "winterized" by nursery, pruning almost all new growth.

I repotted it, mix of ladybug planting soil, compost and manure. I live in South Texas. So the plant was showing new growth, because we have very mild winters.

We had a night of mid 30's, the plant was moved into heated garage. Then put outside in unusually warm weather (80's)

I get home from being away for 5 days and plant has brown patches. Is this sun scorch? Fert burn (I've only used compost and manure mixed with soil when reported), nutrient deficiency, or something else?

I also was told it rained several days I was gone.

I'm really not sure how you winterize a pepper but this is the wrong time of year to fertilize. If your plant was put into a deep sleep by the nursery you purchased it from, just keeping it warm and watered should have been enough until next spring.

Then you could repot and add a small amount of well composted manure. Emphasis on "small amount" and "well composted".

Was it outside for the 5 days of rain? If so, that might be why its not yet dead - some of the fertilizer got washed out of the soil.

In the spring, I would plant this pepper in the ground. If you have a 30 degree night once in awhile, cover it up. I grew peppers for years against a south facing wall in zone 8. They went dormant but always came back. South Texas is a whole lot warmer than Northern California.