Let the eggs sit for 12 hours minimum first, if the air cells are still broken after that, I wouldn't look forward to chicks hatching from those eggs. The wait beforehand is specifically for situations like this - to let the air cell settle back in place again. If you're already incubating them and indeed the embryos are fine, you should be fine. I always prefer the carton method though. Otherwise you'll get chick pinball in there, or worse. . . I've had some very sticky situations with eggs hatching on their sides before.