The issue of the endorsement changing doesn't change the underlying fare rule. When they had to reissue the ticket for an even exchange they have to manually store the fare. Part of that process is putting the endorsements in, and if they didn't look at the fare, or the previous ticket when endorsing it, it's not uncommon that they just chose the nonrefundable endorsement out of habit since that is the case in the majority of even exchanges they do.