Yes and no, depending on how it was implemented. Certainly, we know only the best males were allowed to breed, so that's already happening. Making sure it was an even 1/12 from each family breeding would actually help increase diversity by ensuring that, for whatever reason, there weren't a ton from Line 5 for a given year and none from Line 11. So you'd have 1 male breeding with (likely) all of the females from the other bloodlines, to the degree possible avoid inbreeding.
Hmm, maybe. I really don't know enough to say how many generations like that they could have before devolving into a genetic bottleneck, but surely it could work for 1900+ years.
They would need quite a few females to accomplish that, of course, and those males would need to have several children per partner to account for those who would end up as defectives, deformed children, etc. and to keep the gender ratios balanced (I'm assuming they would still have 50%-50% odds for that, unless there is something in the Nonman genes that interferes with it - who knows, maybe the genes which produce whale mothers also make one of the genders less viable or something).
It would be interesting to know if they also had non-whale mother women being born during those 2000 years. I'm assuming they either didn't or they were all killed in infancy (and whale mothers were the ones allowed to live) given that Koringhus has to explain to the Boy that their "First Mothers" looked like Mimara. He would have worded that differently if there were human-looking women around.
