Originally Posted by
frb98mf
Below is my correspondence. I was inclined to agree with you, but I wanted their ruling, so I explicitly stated that they were separate tickets, merely linked electronically. I then asked my local BA office to link the PNRs (which is pretty common practice) with a note on each referring to the other, and send a single email with the two ticket printouts one after the other, just to be sure I'd adhered to the requirement for a single flight summary, whatever that means, and had them confirm that they would be happy to refund the APD after I boarded the second flight.
[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.