The correct option is D had you been flying
The past perfect continuous form of any verb is obtained by adding 'had been' to the base verb + ing. The verb in question is 'to fly'; for which the base/ root form is simply 'fly'. Applying the above, we clearly get 'had been flying', which is Option C) AND D). The trick here is to identify that the core sentence is a question - and when we ask questions, we sometimes invert the positions of the subject (in this case, 'you') and the tense form. Thus, the correct answer is Option C) and not D) as the latter is incorrect. Both A) and B) are past continuous.