As best as I can tell, this seems to have happened because I logged into my DK first after the pre-patch as opposed to my monk. My monk obtained true friend status with both “factions” and the achievements are account-wide, though technically I should no longer have either if this was intended.
It’s also worth noting that my progress toward 100 exalted reps hasn’t decreased, so in theory grinding these again would have them double dip. I haven’t tested the double dipping theory, though, because screw key farming. I just want my achievements to be reflected in the rep menu.