Sor Sacramento is breathing when she appears to have died. It's possible that she's merely unconscious, and the other characters assume she's lost because they have no resources to save her.
At the end, José María and Fray Vicente exit the building through an automatic door, instead of teletransporting in and out while shouting "cock-a-doodle-doo," as was done throughout the film. It's possible that changes have occurred to the building after the war.