I haven't actually tried to use benefits with AE and credit to A3 (or MP) on AC flights yet (partially because of the Tango fares, I am simply flying a lot less with AC). The typical situation from reading the threads, is that people make their reservation, then do OLCI with the *G FF#, then try to change the FF# after check in at the airport (typically by asking a gate or lounge agent to make the change). This is the procedure I have used on UA flights, and there is considerable evidence on these threads that it will work with AC. Obviously, you have to be cautious because as reported in threads above, there are certainly cases where AC agents (gate or lounge or otherwise) have refused to change FF#s.

Obviously, you can leave the A3 number in the reservation and then try to obtain benefits with your AE*G, but there are many instances where FTers seem to report that this is less successful, or frowned upon (perhaps with the exception of lounge access, where it seems that it doesn't really matter as long as you have *G and a valid *A BP).

As far as I can tell, the reason for this is because if you have used your *G FFP for baggage, priority seating, upgrades, etc. it is far less likely that you will be denied a switch in FF# after the fact, whereas trying to do so upfront with a different FF# on the reservation/BP appears to agents to be more "suspicious".

One thing I've learned in trying to navigate this, is that while the perception on FT is that the need to switch FFPs is a 'big deal', it is not the case from the agents of the various airlines point of view. Despite all this attempted migration from one FFP to another, most agents have never been asked to change FF#s, and most that have, have not been asked all that often. Further, in both the case of UA & AC, very few agents (lounge or otherwise) appear to have ever seen A3 cards or are even aware of Aegean's existence. There is plenty of anecdotal evidence for this on the forums, but it is also my own experience at least 10 times with UA, AC & US - both in lounges and with other agents. The rarity of these types of requests from the agents' point of view, makes it all look suspicious.

If you read the threads I posted above in detail, you will note that carriers across *A theoretically have access to two fields on the reservation: FQTV and FQTS. These fields are for FF#s - one for benefits and the other for mileage accrual. The problem is that some airlines have a policy not to use them (ie. US) and UA's post-merger systems (inherited from CO) have removed them. I believe AC still has them, but it may be very hard to get AC phone agents to input the proper FF#s in your reservation because they likely will have no idea what you're talking about when you phone, but I suppose it is worth calling and trying a few times. If your booking is with a travel agent, they may be able to access the fields.

The next time I fly US, knowing their policy, I will NOT input FF# at booking and try to keep my BPs blank so as to attempt retro-crediting and obtaining benefits by using my card during the actual trip, as I am reasonably certain thats they will refuse to make any changes (certainly, they persistently refuse mid-itinerary, unlike UA).

I know the anxiety this causes when you are trying to make the change, using benefits that you've clearly earned in the previous term/year/whatever, but you just have to try your best and then report back here with the results. I, at least, will be interested to know the results of your efforts.