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I would imagine that the personnel in airline ICT departments who are entrusting with the API data transmission side of their networks have had to undergo stringent enhanced security clearance. I would also guess that how the data is transferred airline to government is over a very secure, encrypted, confidential network detached from the airline's other networks (in a similar manner to the military having a confidential network for sensitive applications and data). Bearing these assumptions in mind - lets face it, no one except those directly working within the system will know how it works and the security involved - it would take a very determined, inside man to get at your information.
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You would think so, wouldn't you - unfortunately this is often not the case, and it doesn't matter whether this data is processed in the UK, or the EU, or wherever. Remembe that the reported cases of data loss & theft are only the tip of the iceberg - but I don't want to hijack this thread, so will leave it at that.