Incorrect 1099

Why would you do the 1040, if the C 1120 for that same year was yet to be prepared?

It seems there is more trouble than just: issued a 1099-Misc to the SSN. Look at this statement:

"I find out that my client was issued 1099's to her social security and to her old Sole Prop EIN in addition to her C Corp EIN"

Are you stating some things are double-reported? Are you stating there is a Mix of reporting? The Sole Prop EIN is just an alias for the SSN, so unless that is double-reported or self-overlapping, those two, in itself, isn't part of the problem here.

And your client needs to be counseled on Contracting, because the SSN should never be provided; she is an Employee. Imagine if any employer is revealing employees' SSN to their own customers.

"She was incorporated in 2017 and asked all Payers to use the new EIN"

By issuing a Letter on letterhead, for the new corporation, and including a W9 when asked for, so that the client has it all on file? It is likely your client isn't signing legally as "President" or some other title indicating that the corporation is a separate entity from herself, which is done for legal and protective purposes. Why form a corporation when you don't honor the purposes?

This person needs legal and financial counseling. Have you considered what her insurance policies, vehicle titles, debt obligations, etc, all look like from the perspective of Name and Title of the responsible party? Has she been using her personal car for business and letting the corporation pay for all operating costs, for instance?

And the reason I would never work on the 1040 until the 1120 is done is specifically because of common mismanagement and commingling issues as you see happening here.