Since payroll is already in 2017, all the employees that you have entered are set for calendar year 2017. So, yes, when you actually reach 2017, all will be well. Since you are not producing real payrolls for 2016 (e.g., no 941 or W2s), the fact that the payroll is set for 2017 and the employees the same, you do not have an issue from what I can tell.
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