If the COC, which includes the fare rules by reference, requires that each segment be flown in the order ticketed, e.g. by "coupon", the remaining coupons should be cancelled should any one not be flown. This could be avoided:

1. By a failure of a single carrier's IT. Not likely on either BA or AA, where their IT does permit relatively immediate cancellation, even if checked in for a subsequent segment.

2. By failure of multiple carriers' IT to communicate. Not likely between BA and AA which do communicate very well.

3. As with all tickets, by changing the ticket with the carrier. This is not about "skipping" a segment, it is about making a change. This may or may not be possible depending on the fare rules and it may or may not carry a fee, depending on the fare rules. And rules aside, a carrier may waive the prohibition or penalty.

But, the bottom line is that if the rules provide for cancellation, one must be prepared for cancellation. One cannot obtain protection from this happening in advance other than by making and paying for the needed changes.

The upside is that one might slip by. The downside is that it won't work and one must purchase a new ticket for the remaining segments and take whatever credit there might be from the cancelled ticket to pay for it. If that cancelled ticket was fully refundable, the credit would actually be a refund to the original form of payment (less any service fees, if applicable).

All about risk tolerance.