I don't know how to link the fare rules. I saved a .pdf of them and here's the language about changes after departure.

//CHANGES AFTER DEPARTURE//
THE ITINERARY MUST BE REPRICED USING HISTORICAL
FARES IN EFFECT ON THE PREVIOUS TICKETING DATE.
--------------------------------------------------
THE NEW ITINERARY MUST MEET ALL RULE PROVISIONS
OF THE NEWLY TICKETED FARE - I.E. ADVANCE
RESERVATIONS/TICKETING DEADLINE/MINIMUM/MAXIMUM
STAY/BOOKING CLASS/SEASONALITY ETC.

Departing MUC on 11/29/16 for ORD
Fare basis code IKN4S4T1
Flying AA
Booked 9/9/2016

The fare allowed departures from MUC and returns to GVA/ZRH.

Edited to add:

I found the booking code detail in Expert Flyer and under the exceptions, it says this

VIA AA D/J PERMITTED I- FARES BETWEEN LON-EUROPE
FLTS 6246-6779

The AA codeshare flight numbers for the BA LON-Europe flights that I want fall into this range.

Does this mean they're permitted for my fare, and if so, how do I explain this to an agent?