I was in same situation as you in 2006. I had made all the documents ready to apply for H1 by April. I was planning to submit the application and go to Nepal in May. The lawyer came to know about it and recommended me to submit H1 application as soon as i came back in May. Luckily I was back few days before the quota ended and I had make the copy of new I-94 and send it to the lawyer. I would recommend you the same, because when you leave US you will have to give the current I-94 at the airport. And by the time your H1 will be processed, that I-94 may be not in the system.