The more I think about it, just because something is inelegant doesn't mean it's wrong. The fact that there is a rule telling you to discard a shadow card when its enemy is defeated suggests that you don't discard a shadow card from an enemy that is not defeated. You only discard the shadow card from enemies that were not killed at the end of the combat phase. 1.42 can still fit in within that framework. As for the order, I think the intention would have been to discard them in the order in which the enemy attacked. But they haven't said that so 'first player chooses' kicks in. A player may decide to discard them in the order in which the enemy attacked, but it's not compulsory.