Once you've keyed in your employee's Resign Date in his/her profile, you will notice that the resigned employee's name will still appear under Payroll > Payroll Settings > Step 1 (Select Employees) but the box will be auto unchecked.

(Employee Profile)

(Payroll)

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By default, the resigned employee will still be displayed for 3 months after their Resign Date.

For example in this case, if you select February 2023 payroll in Process Payment - Step 1 (Select Employees), you will notice that the resigned employees will no longer be displayed.