... took out all but two QC. I left best looking one that was sealed and one that was not sealed but had larvae within as a contingency. Hopefully once the first one emerges she will do what she has to do. ...
If you leave more than one cell in a hive there is the risk that there will be an afterswarm ("cast") losing you half the bees in that hive.
Hence it is best to reduce to just one cell - and to ensure that one is good and healthy, it needs to be UNsealed. Once its sealed, you don't know for sure what state its contents might be. (So some advise leaving two if they are all sealed.)
Since you have another functional colony, I'd suggest that you reduce to one QC to remove any risk of losing bees. The presence of the other colony means that you aren't in any real trouble if that single QC fails.
After the Princess is due to emerge from her cell, you should not open them up or otherwise muck around with that hive for about a month - to allow time for mating and starting to lay.
You can't go in to check that the second QC has been 'dealt with' by the first to emerge.
Tidy up ASAP.
Large colonies do best. Small colonies don't do much; their effort is all taken up with 'overhead cost' and they never turn a profit.
50,000 bees in one colony will bring in a lot of honey beyond their own needs.
Two colonies each of 25,000 will produce a total crop that is very much smaller.
If you intend splitting your colonies, build them up first.
Good luck! Keep us posted
