While BA.com only asks for one passport, it's actually possible to enter multiple into Amadeus, all for the same person. Extras would need to be done over the phone/at the airport, or via your travel agent, but in this dummy booking I started creating below, I have entered a GB passport, a US green card, and a CA passport: the 2nd passport could be any nationality, I was just playing. The lines can be associated to a specific flight (the S2 on the end of the passport lines) or not (the green card) - if a segment is specified it only applies to that one, if no specification, it applies to all of them.
I believe all the API gets sent to the relevant countries involved, so surely a bigger picture helps authorities understand how a resident/dual-national left/entered a country?
(I don't personally have a 2nd pspt, only GB and then a US green card, but I often see PNRs with multiple passport SSRs, and have not heard of any issues. The point is, Amadeus can take it…)
Code:
--- RLP SFP ---
RP/JAXBA080F/
1.KING/JOHN LORD
2 BA 066 J 04JUL 5 PHLLHR DK1 1830 0640 05JUL E 0 351 M
3 SSR NSST BA HK1 PHLLHR/01A,P1/S2
4 *SSR FQTV YY HK/ BA00000001
5 SSR CTCE BA HK1 PRESIDENT.EMERITUS//BA.COM
6 SSR CTCM BA HK1 19041234567
7 SSR DOCS BA HK1 P/GBR/123456789/GBR/29AUG17/M/01JAN30/KING/JOHN/S2
8 SSR DOCS BA HK1 P/CAN/123456789/CAN/29AUG17/M/01JAN30/KING/JOHN/S2
9 SSR DOCS BA HK1 A/USA/A123456789/GBR/29AUG17/M/01JAN30/KING/JOHN
10 SSR DOCA BA HK1 R/USA/S2