@BigRedConsulting  posted this in another thread.  

I just built a free little utility that bypasses the QuickBooks restriction and lets you set the SSN to nine zeros.

See https://bigredconsulting.com/products/employee-fixer/

Once the employee is updated then the W-2's print "Applied for" as expected and required.

Hope it helps, since Intuit/ QB won't.  

Here is the link for the thread I mentioned.  

https://quickbooks.intuit.com/learn-support/en-us/employees-and-payroll/how-to-add-an-employee-who-h...