I'm struggling with similar problems. I got a feral colony from a barn about a month ago. A week ago, I bought a nuc.
The bees in the nuc are working hard and drawing comb. The barn colony is losing numbers (there are only capped drone cells and a few larvae from what I think is a laying worker) Tonight, I checked the nuc and found three uncapped queen cells on one frame with some spotty brood and larvae. So, I pulled the frame with the queen cells, brushed off the bees, and put it in the barn bee hive.
Now, I'm having second thoughts and wonder whether I should have done that. The nuc still has brood on two sides of two remaining frames, pretty solid pattern on one side and somewhat less on the other. My fear is that by doing this, I'm risking both hives. (I have no idea why the nuc is building queen cells either. I have trouble believing it's queenless.)
Any advice?
kev