I would not worry to much for the first couple years. after that you could swap roosters.
Different story with, Hogs, cows, and some others.
Rabbits are a different story all together.
I can tell a little about rabbits.
If you breed mother to son or daughter to father. Then the litter will tell you kine of blood line you have in the parent buck and doe.
If all the off spring from this breeding turn out good then you have a good blood line.
If not, you will have high mortality rate, slow growth, deformed, etc.
DO NOT use any of this litter for breeding purposes even if they all turn out fine.
One more on rabbits.
Do not breed direct brother and sister. half brother and half sister is ok the first time. But try to get father away the next time. cousins is fine.
Have at least two does, and if possible two bucks, but one will do.
The father daughter, mother son litter should all go to the cook pot.
The only purpose for that was to check your blood lines.
If the litter shows bad signs then you need to get another buck or doe or both.