Re: swarm cell surplus
dp, by allowing them to keep one swarm cell she will leave with the prime swarm, usually as soon as the swarm cell is capped. A hive will have after swarms as well depending on how many more swarm cells are in the hive. If your desire is to keep this queen then you should either remove all swarm cells or remove her and a portion of the other bees to new hive and let the original hive requeen with 1 or 2 cells. You did not mention if the queen cell that you left in the hive was capped or not, if it was capped then she has most likely left with a swarm, if so don't be too concerned, you do have her daughters and they should have her genetics.
You stated that you did not understand why the bees would replace her, well its their way of procreation.
Bill...in Southeast Ohio Zone 6A, Never look down on anybody unless you are helping them up