The OP is in a fairly unusual situation .. it looks as though the colony may be trying to supercede but you can never be sure. The risk that he faces is that the bees know better than him and may have recognised a queen who, whilst currently laying. may be imminently failing.
Knocking the queen cells down had a risk that there could then be a queen that failed in the hive and without fresh eggs there would only be the possibility of a scrub queen in this situation.
Keeping the queen cells but isolating them from at least part of the colony is an insurance policy - it is, of course, possible that they won't emerge and a further risk that, this early in the season, they may not get mated or get mated without the volume for a queen with longevity. In this situation then two the colonies could be combined and very little is lost.
On the positive side.. there are signs of drone cells in some hives I understand and if the virgin finds a mate or ten when she goes off on her mating flight there is the option of using her - if only long enough to check whether the original queen continues to lay or fails.
Of course, it's altogether possible that a capped queen cell could be empty - I've seen this in the past - but they don't usually cap queen cells full of Royal Jelly so I think there's a queen in waiting in there.
The OP was fortunate to have a mating nuc which allows him to keep the queen cells without really affecting the main colony. I think he's done well and I will be interested to hear the outcome. Great beekeeping ...and interesting too.