CIS paid to wrong business account by contractor

I have a sole trader business (that is now inactive with no turnover and ready to close) and a Limited Company which evolved from the sole business. It was realised upon preparing the company accounts that a contractor had deducted and paid the CIS deduction to the sole business and not the Ltd company as should have. (The CIS statements were made out to the ltd co, they had simply stated the incorrect verification number on the statement. I rang the SA helpline and was advised that we should claim the payment back as a refund upon the SA return, stating details as to why this happened. The work done for this contractor had gone into the company accounts and the corp tax paid thereon. I have now received a letter from HMRC saying they have amended the tax calculation for this client, and that the sole business has earned that self employed income from the contractor and therefore is to be taxed on it. I really am unsure who I need to speak to regarding this, it was the SA helpline that instructed me to do it the way we did, and now that appears to be wrong? The only reason the sole account wasn't closed was due to this (I can see the contractor has done the same again in the next year, despite being told of the problem) Do I ring the helpline again, or the CIS helpline? or do I need to write to someone? Any advice would be greatly appreciated, I spent every day last week trying to get through on the phone without success. Many thanks in advance

Hi,

Generally spreaking, as the CIS deductions relate to the limited company, the CIS suffered should not have been recorded on the Self Assessment return. An Employer Payment Summary (EPS) should be submitted via the limited company payroll to report the deductions suffered.

If a CIS repayment is then due, you may be asked to send the payment and deduction slips alongside bank statements so the amount can be verified.

With regards to the individual tax calculations you would need to contact our Self Assessment team.

Self Assessment: general enquiries

Thank you.