I think you should make it very clear to your empoloyer that you will be unable to work from sometime in May until the end of September even if you get H-1B. The sooner the better. If I were you, I would do it now, right this second!

If they already like you, then you shouldn't have that big of a problem. They will probably help you find alternatives. If they don't like you, then you will know it now, which gives you enough time to look for alternatives.