Several things:
"While opposed" refers to Jonathan, not the player.
Because Endor is an instant ability that has already completed, the ITB doesn't undo the exchange. Spy stays in battle and Jonathan stays where he is. If it had been a straight "negate an evil card", then Jonathan would come back.
Cards cannot gain or lose CBX after they are played*. Say that Spy plays an enhancement which negates Endor (Bravery of David when Dave isn't in play, for example); Jonathan would come back and make OT red enhancements CBN, but BoD is still negatable because nothing was making it CBN when it was played.
*Unless they're characters; they can gain or lose CBX after they are played by entering battle. For example, placing Joy on Music Leaders doesn't make it CBN because it was already in play and can't gain it; however, if you then attack with Music Leaders they reactivate and gain CBN from Joy.
