Two queens a-laying (in one hive)

We have found this a very tricky season for queens; beyond all the normal swarming issues, we have also had hives that have superceded their queens without any sign of swarming and twice had hives that suddenly are found to be queen is missing and there are no queen cells to replace her. Then, in mid August we suddenly found that one of the hives has two queens happily both laying! We had merged the last of the swarms into one of the main hives and still had the two brood boxes stacked on top of each other but had reached the stage where after the colonies had merged we have put the queen excluder back over the main brood box and were ready to remove the top one. This is when we discovered that we had a queen in each box - not that I could find either one but there were eggs both above and below the queen excluder.  I have read about such things but its still very strang to see.

There has been so much turnover of queens that 3 of our 5 hives are only just big enough to survive winter and have not produced any honey in the supers but they are on commercial brood frames and have plenty of honey in there. We will keep monitoring them are now hoping that all the hive settle down in time for winter or we will have to do some final merging.