If you have multiple segments only the segments that are changed will be repriced, the others will retain the discount. Keep in mind that a through fare on two segments are "married." Changing only one segment will void the discount on the other as the through fare will be repriced without the discount. I was experimenting with this online.
On a return ticket, if you change the outbound and retain the return only the outbound should be repriced. My ticket was 6 segments, effectively 2 segments to a stopover and then a return with 2 segments in each direction, a little over 6K miles flown for a base fare of $177. Stupid Cheap!
I was able to change the first two segments to just about anything I wanted including creating an open jaw and international travel. The reprice was only on the changed segments.
It was a great promotion but I think AS erred in allowing a 50% discount to a single passenger. If the intent was to be a companion certificate for public use, the provisions should have required two passengers for a valid query as the companion certificate does. A single passenger discount doesn't really harmonize well with a BOGO "GETTHEROW" promotion. I am not surprised they are steadfast on changes. I would anticipate AS would accommodate on a segment cancelation, swapping one segment for another without repricing.
I canceled my itinerary as it didn't work out for me after changing my desired destination. Had I flown it, the itinerary would have generated 9,392 EQM for a base fare of $177. That is $29.50 per flight segment. All segments were within the US.
James