Re: Dumb, Dumb, Dumb!!!
As per MB you have not wasted the cells you've taken out insurance.
In fact, sounds to me like the original queen cells were produced by the bees from eggs laid by a worker. The larvae in these cells are male and perish immediately after capping, and the bees tear them down quickly as there is no cocoon. If there was no other normal brood in the hive at the time, this is what happened.
And agree with MB again, the eggs in the 2 queen cell cups you found were almost certainly male, from a laying worker.
So putting the brood and other queen cells across was exactly the right thing to do.
"Thinking Inside The Box"