I know next to nothing about aviation, but am wondering if it is possible that an electrical or computer malfunction (or a computer system virus?) could result in shutting down the transponder and the navigation systems and leave the crew confused as to where they were? If this were the case, why wouldn’t communications work? I would think that if they flew for several additional hours (as per the automatic updates communicated from the Rolls Royce engines) they would have tried to contact someone regarding their actual position.
No single failure should be able to take out all those systems. There are several means of communication off the aircraft and nothing should be able to take them all out at the same time short of total power loss or something else catastrophic. For someone to have done it deliberately is somewhat easier, but it would require a good working knowledge of the aircraft.