I'm getting the same. I went back and re-flew earlier Dragon missions and there was no problem or conflicts (and no disappearing Dragon).
BRB, I got an idea...
OK, I think I've got it. Delete the Dragon (cargo) that is currently docked to Neesys. It would appear that you can't have 2 Dragons of the same make/model in the same scenario, or at least not in the way presented here... At least deleting the cargo Dragon allowed this particular flight to work out anyway.
I'm updating the "bonus mission" to not only do a flyaround with the PTV (while Endeavour is on station), but to deorbit the Dragon cargo as well (maybe adding to the down-mass that Endeavour is bringing home perhaps? Anyway, this way the scenario should work.