I understand it wasn't inaccurate. However, if we make the S-Election, backdate payroll, etc., then we run in to the issue of the 1099 being issued to him/his disregarded entity which now would be incorrect.

I am asking to allocate it to the other entity, yes, however, I know this will lead to reconciliation discrepancies when his Sch. C for part of the year doesn't reconcile to the entire 1099 amount. The entity name was not listed on the 1099s, as his accountant failed to instruct him to submit updated W-9s after the LLC was formed (which I understand, IF operating as a disregarded entity wouldn't matter much).

There is a bank account for the LLC that was utilized.