How wonderful in a horrible way - presumably the bats weren't coming through the 'new' entrance, so if it's made weatherproof it shouldn't entomb them? Crumbs, I think that's about all you can do ..How luverly tho', once it all gets sorted. We had Sussex Batlife (or similar) along to our local Beaver Scout pack with a variety of bats for the children to stroke - they purr! The Bats, that is, have a 'pleasure purr' like cats do - if you can get close enough that is!
Let us know how you get on?