I'm sorry to hear you lost your passport. You should file a police report for your passport if you think it was stolen. After you have your passport replaced, if you are chosen for the H-1B, when you leave the USA after your H-1B is activated in October 2014 you will need to get an H-1B visa before you reenter the USA. If you choose instead to remain in school, you can speak to your school officer about issuing a new I-20 for the new PhD program. If you decide to travel, then you will need to discuss the timing of your travel along with applying for a new F-1 visa in your new passport. Good luck.
This answer is provided solely for informational purposes only. You should always speak directly with a lawyer. This answer does not constitute legal advice or create an attorney-client relationship.