So, I tried searching around the forums for this question, but couldn't come up with the answer, though I found a few discussions about it.
Basically, does End of Days destroy the cards underneath La Capitan? A lot of the careful language on similar villains (Mad Bomber Blade, for instance) which specifies that the cards are indestructible, not considered to be in play, etc. is not included on La Capitan. I wasn't sure if this was an intentional omission to indicate that La Capitan functions differently, or simply the fact that she's from an older set.