Agreed, if both queens are in the hive laying it will explode with bees very soon.
The question is, do you wish to weaken your strong hive to bolster your weak hive?
If the strong hive is on the verge of swarming, it can be a good thing, if it is not, then I would let them be and get as much honey as I could from the strong hive. If the weather and other conditions permit, the weak hive will catch up.
The best reason to have two hives.. seeing the difference between them.
Next, is the ability to steal a bit from the strong to bolster the weak... BUT, the weak is weak for a reason... Superseding the queen is a valid acceptable reason. If there is a new queen, and she is doing WELL, then giving her a boost might well catch that hive up for the fall flow.