Just a chance for everyone to pool their theories. Here is mine.
I am going to assume that Unohana's and Zaraki's flesh melting wasn't a metaphor, but Minazuki's power. First, I am surprised that Unohana can be damaged and potentially killed by her own Bankai. My theory is that everyone that comes in contact with the blood released by the sword will be melted to their bones. Not so original up to this point. However, I believe that the blood that is spilled due to Minazuki's effect will be absorbed into the sword when it is sealed again, so that the amount of blood it releases grows larger every time Unohana fights. I think imagining it as a "cumulative" Bankai that gets stronger over time (also relying on Unohana's passion for battles and mirroring it and her self-destructive spirit of all Kenpachi) could explain its incredible power, as we have seen that it takes mere moments to be reduced to a skeleton, and the fact that Unohana herself could become a victim: just like the Shikai shows her "caring", "medical" side, the Bankai is pure, all-consuming bloodthirst.
On a totally separate note, my theory is that the Asauchi had just been developed when she battled Zaraki, and that she still didn't know her sword's name at the time. Considering Unohana was still the first Captain of the Eleventh Division, it might be possible, chronologically speaking. Incidentally, this would make Zaraki one of the first Shikai users in Soul Society.