Can someone help explain how earning Avios works when you fly a OneWorld partner airline - where a booking is combined with another partner airline, but that partner is a Star Alliance partner (man, that's confusing!)?

The reason I ask is that my spouse is in the middle of a business trip to HKG and SIN, and both his Aeroplan and BAEC numbers are recorded on the itinerary, but he's missing his Avios for the CP flight. Perhaps they just take a while to show up for partner flights? Here's the dates:

April 19/15: JFK-HKG (CP - No BAEC points showing on account)
April 21/15: HKG-SIN (SQ - Points showing on Aeroplan)

If the miles are missing simply because his BAEC number got lost in the shuffle and didn't get recorded for his CP flight, is it possible to get them later? And what, if any, documentation would be required as proof (boarding passes, itinerary, etc)?