Can we file for H1B transfer while H1B amendment in is process

Hi,

My H1B visa got stapmed for company A , client X while in India. But later on I travelled to US while working for the same company A , but for client Y at a different location and a Non Premium amendment has been raised for the same. I was issued the work authorization letter and LCA for client Y based on which I have travelled and have been working since last 2 months. Currently I have a job with company B whch is ready to sponsor my H1B. My question is, can the H1B for company B be filed since the earlier amendment for company A and client Y is still in process?

Can my visa get cancelled in any way?

Please help.