She will not like to mate with foreign drones, and will actively kill them. This is explained in the tutorials for the bees.

She has very particular tastes. They must be the same species she is.

https://frackinuniverse.miraheze.org/wiki/Bees

I get that it'll happen with foreign drones, but I'm just breeding Crystalwings with Crystalwings, of the same subtype. Is the new queen just always going to kill the old drones as she generates a new generation of them? I don't understand why I should save the lives of the old drones if they're just always going to be killed off anyways while generating a new generation. How does one generate a stack of thousands of drones if they're just going to be killed off every time?

I'm not trying to be dense, I'm just trying to figure out how this works. I'm just seeing a cycle where every new queen generates a new stack of drones from the old drones and gets to around 250 before she dies.