"Thought that went without saying but yes, the payments and reporting were sent."

Never take anything for granted when you find these types of errors 🙂

Is this the only person working in that business?

There is no way to do payroll under their SSN, so they sent in Employer taxes for their FEIN, which you need to apply to be refunded, along with the "employee's" money. The accounting expenses are wrong, too. The easiest way to handle this is to take all the entries that are payroll and change those amounts to Owner Draw. Then, when the funds come back, the owner can use it to help pay the taxes he owes. He likely wasn't making quarterly estimates and didn't know to have a plan or keep track; otherwise, this might have come up sooner.