The princess is (as said before), either the original species, the drone species, or a mutation (good or bad). You can't mutate your way "back" along a branch, but you can overwrite.
My suggestion (and what I ended up doing):
Find a load of pure bees (Forest, Meadows, Marshy, Tropical, Wintry, etc.). For each of them, pair the princessess and drones, and make a repeating hive (princesses/drone automatically taken out, and put back into the same hive, excess stored elsewhere). This will amass you a stock of pure, basic drones. You can typically overwrite a princess with between 2 and 10 drones (depending on how lucky/unlucky you are). As you go up the mutations (common, cultivated, noble, etc.), attempt to purify the species, and get a breeding pair of pur bees. Add those to your stock.
This means that you can have a set of "experimental" bees, and a set of "producing" bees. The experimentals can be rewritten and changed to try and produce a specific mutation, rather than trying to take a hive bee from basic to the top tier in one go.
Just to be sure, what I mean by rewriting is that you can take a stack of, for intsance 10 drones, and put them in the drone part of the apiary. When the pipe tries to put the descendants in, it can't because the slot is full, so they go off to storage. The princess is inserted, and they breed.
If you start with a pure diligent princess (which you don't want), and put a stack of 10 cultivated drones in, the first mating will be pure and pure, with approx. 50/50 hybrids, the second will be 75/25 in favour of cultivated, and the third will be 87/12. This changes due to the chances and mutations, but, as I said, it usually only takes a few cycles for a complete overwrite.
