The high risk audit alert is because if wages were actually paid, then there should also have been employment taxes paid. In your case, you didn't actually pay payroll and payroll taxes. So I wouldn't worry about the alert when you zero'd out the compensation in your case.
You could make the case in the COVID environment that you paid yourself as a consultant and issue a 1099-NEC (formerly 1099-MISC box 7).
Report on Schedule C on your personal tax return and pay the self-employment tax there. Amend the 1120 to move the compensation to Other deductions.
