H1 transfer without working for the company which did the H1

[Kabirdas64]

Hi,
I have seen similar topics but couldn't find exact scenario as mine. Hence writing a new post.

I am currently in US on L1 with Company A (L1 already expired 1 year back but have a valid I-94 till end of 2016)
I have applied H1 thru Company B (consular) but didn't get I-94. So I am still with Company A and have never worked for B.

I have talked to Company A on the H1 thing with Company B. Company A says that they can apply H1 transfer. 
Will there be any problem since I don't have pay stubs from Company B but only pay stubs from Company A.

Will this in any way impact GC processing (to be done by Company A)?

Thanks
Kabir