Lunar oracle and calistra's boon

"Do ability modifiers from the same ability stack? For instance, can you add the same ability bonus on the same roll twice using two different effects that each add that same ability modifier?
No. An ability bonus, such as "Strength bonus", is considered to be the same source for the purpose of bonuses from the same source not stacking. However, you can still add, for instance “a deflection bonus equal to your Charisma modifier” and your Charisma modifier. For this purpose, however, the paladin's untyped "bonus equal to her Charisma bonus (if any) on all saving throws" from divine grace is considered to be the same as "Charisma bonus (if any)", and the same would be true for any other untyped "bonus equal to her [ability score] bonus" constructions." ~paizo core rulebook faq

Agreed. The Lunar Mystery allows you to use your Charisma Modifier instead of Dexterity, but your Dexterity modifier is applied to your Armor Class, so in this case it really is just two instances of "Add your Charisma Modifier to your AC" and so wouldn't stack.