OMG....thank you for posting this!!! We had a ghost pepper plant. All summer we got great RED ghost peppers from it. Starting in August we got YELLOW ones, yes they were ripe. We e-mailed the New Mexico Chili Institute and we were told this was impossible!! Ahhhhh....hello....the plant is right here on our deck!! And tell ya what, the yellow Bhuts were hotter then the red ones!! So Nick, am happy to see you post this!!!

I am not alone!!!
Cindy

Cindy save the yellow seeds. save some red ones too but keep them separate. try to keep the plant alive.

try to root a cutting of the branch that has the yellow ones. keep it alive.

many times plants mutate on a branch only. the mutation will only be on that one branch. if you cut off the branch and it dies you have a problem.

Are you saving all the seeds from the yellow ones. It could give you a new variety. This happens all the time. Dr Bosland at the Chile institute will want to help you. you must have talked to someone in the office who does not know anything about what they are talking about.

You would have the only Yellow Bhuts. They will sell like crazy. You can patent the yellow Bhut and become a millionaire.

There already are strains of Yellow Bhut out there.
Some are hybrids and some are natural mutations.
A lot of them are producing stable seeds.
I have a couple of the stable varieties.
Stable Yellow Bhuts have been around for a year or more,same with chocolate crosses and possibly chocolate natural mutations.
In my experiance there are Red,Orange,Yellow,Black and chocolate Bhut Jolokia out there that are stable crosses and Mutations.
I've got most of them.

Depending on the original pepper genes of whatever pepper Nick is growing(hybrid reverting back to it's roots or a mutation) I'd isolate buds and let the plant self pollinate hoping to get the yellow pods.
Red is a real hard thing/gene to get rid of in a peppers color for some reason,in my experiance with crossing plants.
I'd guess his color variations are due to growing conditions rather than a gene thing.
I think all the pods would be either yellow or red on the same plant if it was a gene thing.
I'm not an expert but dissagree that a specific branch will grow yellow pods verses a red pod on the rest of the plant due to a genetic trait that can be passed on in the seeds.
If a specific branch was diseased or defective in some way ,maybe it would put out different pods but wether the seeds had the same traits , that is debatable.
There used to be a tulip(i think it was) that was a certain color that only happened if the plant had a certain disease or fungus.
It was very rare until through years of breeding they got a stable plant from breeding a ton of different varieties to get the same colored tulip.

For instance,I have a Bih Jolokia plant that put out yellow pods when other plants from the same plants seed put out orange pods.
It could be an enviornmemtal thing.
I had a huge mite infestation last season and had plants putting out all kinds of wierd pods.

Example:

http://c2cpeppers.proboards.com/index.cgi?board=others&action=display&thread=2097

The first pods were from a stressed plant,the others from the same - semi recovered plant.

Not knowing if the original plant was a Hybrid or if aphids or whatever diseased the branch of the yellow pods,it's hard to say what you'll get.

If you have a branch thats messed up causing the yellow pods then clone it but it won't neccesarily insure seeds to grow yellow pods because it's not a gene thats causing the yellow pod color,just the branches ability to supply whatever the pod needs to make red pods.
At the same time,hedge your bets by isolating the buds to see if it might produce seeds that do grow yellow pods.
As I said I'm not an expert so I might be wrong.

Hope this helps you be less confused about nature than I am. LOL
Every time I think I have things figured out something different happens.
isolate buds and clone the branch and report back on what happened.

If you are cloning stuff,in my experiance a rooting agent that worked for me on peppers was to mix Root Tone and take root together.
root tone is 1-naphthaleneacetamide , thiram
take root is indole-3-butyric acid
Each by itself didn't work well for me but the mix did/does.
I haven't tried it yet but Dip'n'Grow has both in it.
Should work I'd think for peppers.
Easiest way to clone is to dip a cutting into rooting hormone then put in a jar of water with an aquarium air stone.