None that I'm aware of have anything resembling our modern idea of race built in. For the obvious reason that approximately nobody in said village had been 100 miles, nevermind to another continent. If a language had such a feature, the next generation would probably never have heard it used, and thus would not know what it meant. (I wonder whether any languages have grammatical markers for slavery or caste? That would be the closest thing I could imagine, divisions that many people would have talked about every day for millennia, in some places.)
Forgetting features seems to happen much quicker than acquiring them. Post-1066 English lost a lot of complication which German retained (including grammatical gender of nouns, IIRC). As you say, singular you is much younger than that, but importantly it's about forgetting a distinction we used to make. I'm not an expert on why this happened, but I didn't think it was some great shift in what needed to be communicated, just a mutation/simplification.