Hm. Right now I'm just trying to get past Common. I've already got a genepool up, and I've been feeding the hybrid drones to it. Still not quite sure what the point of the hybrid princesses are. Wouldn't I want to get to Imperial and Industrious bees before I start worrying about traits?
Anyway if you're going for mutations your princesses should always end up pure bred.
And before Imperial there is the majestic bee with the high fertility, that's probably my most valuable serum
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As for hybrid princesses you would have for any reason and don't need to create a purebred line, you can always drop them in an automated apiary with a stack of purebred drones you want to duplicate and the princess will end up pure bred too after several reproduction cycles.
edit:
Do you have a purebred common line?
If yes make it reproduce in an apiary until you have a bunch of drones(they should stack if it's purebred).
You then take any normal bee princess(meadow, forest, etc) and use it with your common in an apiary with 3 soul frames.
You'll probably end up with hybrids like:
princess: cultivated/meadow
Drone 1: common/meadow
Drone 2: cultivated/meadow
You take the princess and Drone 2(which both have cultivated) and put them in an apiary with an oblivion frame(optional but it really helps, found in dungeons at the start of the game, or in loot bags).
You'll then end up with something like:
Princess: meadow/meadow
Drone 1: cultivated/meadow
Drone 2: cultivated/cultivated
Then you cross the princess with Drone 2.
Note that you may lose the cultivated trait you want during this process, in this case you may want to use one of the previous drones you didn't use that had cultivated or try the mutation process again.
But once you keep breeding them with a bit of luck you'll end up with a purebred cultivated princess and purebred drone.
It's a lot easier once you have the high fertility serum since you have more choices, and hence can push for purebred faster.