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CIS verification

Late CIS verification

We have a client who moved the CIS part of his business to a payroll agent.  We were under the impression that this agent was simply going to take over the calculation and payments of our client's subcontractors but what has actually happened is that the agent has become the subcontractor instead.  So we need to continue to operate CIS on the client's now lone subcontractor.  The change happened 6 weeks ago and the agency verifies as a gross subcontractor.  However, my system, of course, is now showing the 1st 6 weeks as unverified and therefore 30% deduictions are needed.  What are your views on now re-setting this new one up separately with the verification number we have already obtained electronically and re-entering the verification number we have only just obtained for the whole period instead of using it just from this week?  Would there be any comeback from HMRC if we do this, as the subcontractor is legitimately entitled to gross payments for the whole period, its just our software that is not allowing the gross from the start due to the late verification process.

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