Try something like this:
Dim currentEmployees As IEnumerable(Of Integer) = CurrentPayrollTable.AsEnumerable().Select(Function (row) row.Field(Of Integer)("Employee Number"))
Dim previousEmployees As IEnumerable(Of Integer) = PreviousPayrollTable.AsEnumerable().Select(Function (row) row.Field(Of Integer)("Employee Number"))
Dim currentEmployeesNotInPrevious As IEnumerable(Of Integer) = currentEmployees.Except(previousEmployees)
Dim previousEmployeesNotInCurrent As IEnumerable(Of Integer) = previousEmployees.Except(currentEmployees)
Dim employeesMissing As New HashSet(Of Integer)(currentEmployees)
employeesMissing.SymmetricExceptWith(previousEmployees)