Can we file H1B Amendment petition for Change of Status from L1B to H1B

I was on L1B for Company A. I had filed for H1B thru Company B. While the H1B was under processing I went out of US for a visit to Home country and came back on L1B. The H1B was approved in Nov 2012 and the Company B advised me to resign for Company A, which I did. I think I should have insisted on seeing the approval notice. After 10 days of joining Company B, we find that USCIS has not approved COS and did not issue I-94.

Company B urgently filed for a H1B Amendment requesting for a I-94 card in premium processing mode. I am not sure if they filed for I-539 or not.

My questions are as below:
Is the Procedure adopted Correct?
Will USCIS issue a new I-94?
I am thinking I should leave the country immediately. Please advise.

I have seen similar case for one of my friend. That Employer has mentioned to file for amendment as well.

How did your amendment go ?