It would most likely be your petition number, but you should direct this question to your company's immigration attorney.

If the application for changing status from B2 to F1 is denied, how the unlawful stay would be counted?

It depends what happens later, which would control the accrual of unlawful presence.

Under 18 green card holder stay outside of USA to finish high school

Your father will have to petition the son separately after he obtains his green card. There may be a wait of several years.

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Few weeks ago got a email off uscis saying they are moving my case to another office

USCIS has transferred many cases from the Vermont Service center to the California Service Center in an effort to level the work load.

E1 Visa

Yes, that is possible. The main issue will be establishing the company's regular and systematic trade between the US and the treat country.

My H1 got picked and my petition got approved. Employer not providing I797(notice of action) form to me.

This depends on whether the approval also included an extension or change of status, which is your document.

If he is referring to your status during previous stays in the US, he means visa admission stamps, I-94 records and any other evidence that would...

You would need to provide an explanation for the late-filing if the 90-day filing period for the joint petition.

Affidavit of support fee

You must wait for the next correspondence from the NVC. Follow up with them.

H1B application possibility by a different employer after 6 years with I-140 if current extension gets rejected

1. Not necessarily 2.If your COS to H-1B is denied, you cannot late-file a request for COS to H-4. 3. Yes, as long as the I-140 is not revoked.