A game that big can't disappear all of a sudden because it's not possible. The only logical reason why the software disappears as if the PC contains Deep Freeze application that wipes everything unless the installation is allowed, but I don't think that's the case.
When installing Microsoft Flight Simulator X, make sure to carefully choose a partition that has enough space, then note the installation folder, reboot the PC and check if it's there. I couldn't see any reason