If a payroll has not been run in a salary period and you have not used Salary for that period, it is possible to make a retroactive zero tax report.
If you have used Salary during the period but still not run payroll, then Salary will have automatically made a zero tax report. You can read more about that here
To make a retroactive return to SKAT for a period, you will have to go to:
Payroll -> Choose Create extra payroll -> Under type choose Zero tax report -> Select the paryoll period -> Choose Start extra payroll:
Salary will now do the zero tax reporting to E-Income.