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because Trump resumed in the gold shittter from the UK home. Why would they be concerned about bugs while in Turkey, but not elsewhere?

One logical explanation is that there was a relatively minor maintenance issue that was easier to deal with in the UK than in Turkey. There are all sorts of systems on a 747 that don't prevent it from flying, but might reduce the redundancy or comfort in flight.

Another logical explanation is that some of the exotic communication systems that are unique to an AF1 aircraft were not working correctly, and they were more concerned about that in the Turkey region than across the Atlantic.

A third plausible explanation is that in a rush to get this plane into service, they left off some systems to be installed later. But in the course of this trip, they picked up intelligence that suggested this lack of systems put the aircraft in more danger than normal.