Every flight," except" for a local take off and landing practice flight. Every plane must file a flight plan. Especially if the are going to enter another countries air space.
A transponder is a device that identifies a plane on a radar set.
A big plane, such as a Boeing 777, would be big enough that it would show up on a radar scope without the transponder working.
Diago Garcia is a military base/site that may house Nuclear weapons. D.G. would have radar working even from anchored ships to make sure nobody is sneaking in to their facility, just as any military base since the time of the Romans tries to protect itself from sneak attacks.
Therefore, it is my suspicion that any thing within 500 or more miles of Diago Garcia including unknown ships or big airplanes, would somehow communicate with Diago Garcia well before they approached the island.
Diago Garcia may even have the capabilities to fly or control a plane already in flight, such as the missing plane in question. They also have hangers big enough to hide a Boeing 777 from any overhead spying.
Why do I say this? Because if an "unknown" big plane was heading for the island it would be intercepted, or shot down, before it got too close, just in case it really was nuclear.
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