Well, when they fuse to the core in the XIV storyline, they get drained of all their aether and die horribly. Cid's working on a way to save the pilots, but it's likely that we won't save many of them. My money would be on trying to save them and failing for various reasons. Either they know we're going to stop the fusion, so they self detonate or we don't stop the fusion in time. Remaining girl Au Ra will probably not be in a mech, though if she is, it'll be after she incapacitated her brother to keep him safe.