If USCIS has lost h1b the petition(i129) , what should we do?

What happens if USCIS has missed the petition , even though it’s highly improbable. But What happens ? What’s next ?

Let’s say we have Fedex receipt as proof of delivery to USCIS then in that case are we allowed to submit the petition after June 30 ?

You need to mention the relevance of June 30th that you keep referring in your post. How will people know what June 30th means and how is it relevant with your case/scenario.

Sorry April 1 H1b lottery selects get 3 months to submit their petition successfully. so 3 months from Apr 1st is June 30

You can’t submit after 30th June.