When it comes to reasonable compensation for a shareholder-employee of an S Corporation, the IRS isn't concerned about the net income or loss from the business but will focus on distributions made to the shareholder-employee.
If the S Corp didn't make any distributions to the shareholder-employee (regardless of net income/loss) then reasonable compensation isn't an issue. The amount of reasonable compensation that the IRS could reclassify from distributions made will never exceed the amount received by the shareholder-employee, directly or indirectly. Therefore, if the S Corp lost money (had a net loss) but made distributions to the shareholder-employee, then the shareholder-employee should have received reasonable compensation at least equal to the distributions.
As far as resuming payroll, first determine what is reasonable compensation for the shareholder-employee and then resume normal payroll activities as before.
Here is a link to the IRS that discusses S Corp Compensation & Other Issues: https://www.irs.gov/businesses/small-businesses-self-employed/s-corporation-compensation-and-medical...
