most likely the other (old) queen is dead or has left with a small swarm.
As long as you can see lava and eggs in the cells, don't be too phased by this. my bees did the exact same thing this year build queen cells (with viable queens) in the third honey box. very weird but i pulled them when i saw them and made new hives from them.
my thoughts are that they may have just dragged a few eggs up into the top boxes or perhaps their was a few eggs at the right age in one of the top frames....
There still seems to be plenty of bees there. quite often a guessing game this bee caper!