I think it was Alexis and one of the daughters closest in age to Anastasia which they found in a seperate lime pit. The forensic story alone is fascinating.
Here's a pretty good summary with some added details, appears to have been written in 1997. It notes the mystery of the missing two bodies, but all the rest is there. There must be a more complete account somewhere bringing it all up-to-date. I know they found the last two bodies in the separate grave not too distant from the mass grave.