Anything is possible from a lore standpoint, they could retcon a lot of Hrothgar lore, they already did from what I can tell from the little we got in the encyclopedia preview, remains to be seen in December. I already preordered the book and can't wait to learn more!
As for the female Hrothgar being hunted down in the fear that one of them might turn into "Save the Queen", I have already speculated on it previously. Which is not as far-fetched as it sounds since we know how xenophobic the Empire is. The question is if that were the case, it would have started around the occupation so seeing this the resistance immediately must have tried to sneak female Hrothgar out to different places in order to keep them safe. But that must have been hard, looking at the map, Bozja is close to Doma and Dalmasca which we know were already under the Empire's rule, so their only hope would have been to either go to Eorzea, Raz-at-Han or the New World. And since we know that there are Hrothgar in Old Sharlyan, my money would be on that and the New World since we know that there is a trade route from Sharlyan to Tural.
I think, but take this with a grain of salt, that they would retcon the lore quite a bit. From the females being rare, to being more of a 60-40, or something like that, it would still make the females be less in number, but not by such a drastic amount that we get horrified at the implications. And the original lore would be dismissed as inconclusive data since the information came after the Bozjan incident which wiped out almost the entire population, the ones who were spared were the people lucky enough to be far away from the explosion, or the ones who were conscripted by the Garleans. As such very few females, if any got away safely.