Originally Posted by
orbitmic
[Bolding mine] The problem lies in your description: your tickets are not linked. It doesn't really mean anything and what is "pretty common" is not tickets being linked but airlines understanding that when a customer ask that "tickets be linked" (or "merged" or whatever) they just include a note of reference in each booking. This has zero value as has receiving a "single email with the two ticket printouts one after the other".
The airline may have been happy to refund the APD to you but if they did that they were wrong to and if HMRC finds out it will make the airline pay the charge and possibly a penalty.
I wouldn't make quite as firm a conclusion as that. The fact is there is room for interpretation as to what a connected ticket means, and without a court ruling on specific facts we can't be sure (HMRC can be wrong, incidentally).
But that is really second fiddle as far as the passenger is concerned. From our perspective, the difficult built is persuading the airline to refund the APD on whatever 'linking' basis the airline is comfortable with. If people manage to do that, good for them. The one thing we can say for certain is that the airline has no obligation to do this for you when you buy separate tickets.