Troy,
I think if it was me and I noticed bud rot in some of my colas I'd have to cut them (just the effected buds) and get them out of there before it spreads.
I wouldn't throw them a way though. I'd dry them, grind them up and then sautee them in butter or vegatable oil and then use that oil or butter to make a batch of brownie's or cookies.
You didn't say what your temps or RH were but I'm guessing your RH is kind of on the high side for this late in flowering. Better do what you can to get it down.
Although I can't recall exactly I seem to remember reading something about temps under 60F contributing to this. Better do a search on "bud rot" and find out for sure what the contributing factors are.
Good luck.
Jack