The rules state the +2 Health bonus does not stack with other bonuses. The following situation came up in a game yesterday with my girlfriend:

Two skrimishes, one was a Zealot and one was Fenix, a Dragoon with +2 Health. I had a +1 Health reinforcement card in my hand and a Defend token in the area. When she attacked me I wanted to redeem the token to gain +2 Health on the Zealot and use the reinforcement card in unison with Fenix's innate bonus to gain +3 Health on the Dragoon. She argued that by using the Defend token I must use the +2 Health (and only +2) bonus on EVERY skirmish.

What is the correct ruling? May I pick and choose which individual skirmishes in the entire battle to use the exclusive Health bonus on? Or is it all or nothing?

You can choose what health bonus you use (guard token or other health bonuses) for each individual skirmish in the battle when you used guard token. In other words, if you use health bonus from token, you don't have to use it in every skirmish. (if I remember well, that was even confirmed by game designers)