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The particular Appendix 6 scheme is based on estimated pay rather than actual. All of the current seconded employees on the payroll, receive their pay from the home country payroll.
However, HR/Payroll are looking to pay an incoming assignee (from China) 100% of his assignment earnings via the Appendix 6 payroll. I am not sure if this would be a problem and whether it would have a social security impact as there will be a certificate of coverage in place so no liability to NIC.
The guidance is as follows but i don't know whether this necessarily answers the question.
Where the EP Appendix 6 scheme is based on actual rather than estimated pay and is used to deliver earnings, the ‘Deductions from Net Pay’ field should be used as necessary and the Bacs hash code entered for any amounts delivered by the Bacs system.