The best evidence in this case is circumstantial and eyewitness. In the first case, they found intimate objects known to have been on the persons' bodies: the contents of the son's pocket, items customarily carried by him, the belt buckle worn by the father, rings and other jewelry, and most importantly, siix missing women with six different corset busks. (And this is only a minute listing of physical evidence.) As to eyewitness testimony, there are the statements of the person who arranged the murder, the statements of those who participated in the murder, and the statements of those who helped arrange the disposal of the bodies. The primary in this case, Yorovsky, states that in disposal, a fire was first attempted, at which time two bodies were placed on it. When that method was not satisfactory, they buried the two partially consumed bodies, put out the fire, put a layer of clay over it and then covered it with soil. Evidence of fires were found by all investigators, including the most recent excavations at the site. The other grave was found just as described in the statement - including broken vials of sulfuric acid and pieces of rope that had been used to drag them from the mine - exactly as Yorovsky said.
Now, were two people missing from the mass grave? Of course, but that means only that two people were not in that grave, and it means nothing else. It also is the best evidence that supports Yurovsky's statement and the statements of others.
It would seem to me that combined with the physical and circumstantial evidence and the eyewitness testimony, that the reasonable conclusion is that all prisoners in that house perished that night.