I guess you'll have to explain what you mean by 'evidence'. The fact that two bodies have not been found is evidence. Why wouldn't they be with their family? Where are they? That the bolshevik lied in the first place is evidence. Could they not lie again? That the Romanovs were not "buried" in the intented place is evidence. Were the Bolsheviks lax in their attention in getting rid of the bodies? Evidence that there is a flaw in the story, something we have not been told, or evidence to prompt questions as to whether we have been told the truth.
It would seem likely that if the Bolsheviks wanted to continue to lie about this case, they would have stuck with their original lie: that Nicholas was killed but not the rest of the family. You have to remember that the Yurovsky note that tells us about what happened to the two missing bodies wasn't meant for anyone to see, and only came to light recently - when there was no longer any reason for anyone to lie about this case. Some people of course continue to believe that the Yurovsky note was a forgery, but unless it is
proven a forgery we have to assume that it is authentic and that the two bodies were burned separately as stated in the note.
Of course the note could also mean that two bodies were lost somehow other than in the way it was described, but remember, this note was written before anyone knew that the bodies would be discovered and investigated, so why would bring this up at all if you want to cover something up?
Very often in life the most simple things, and not the most complicated, are the "right" explanations... In this case, it seems likely that the most simple answer - that is that they indeed tried to burn two bodies, hence separating them from the rest, seems to be what really happened, unless there is some compelling evidence (not just speculation) to tell us otherwise, which frankly I don't see as being the case.
Perhaps the question of the two missing bodies can finally be put to rest if the two children's remains are discovered by the team currently searching for them in Ekaterinburg... I hope so, although based on the "Romanov remains" record I doubt it will be, even if these remains are found :-/.