Only seen the payroll output reports from HMRC Basic Tools, which were pants, but it was about two years ago. Its the Earlier Year Update you would need to use. BUT - Im hoping Im not going mad here - I understand CIS isnt yet fully mandatory via the online process yet (but thats coming soon), so why not try ringing the CIS helpline to do adjustments over the phone? Fully document time, date of call and full name of person taking message. Plus also provide something for the individual concerned (letter) as thats only fair and correct. Try this number for HMRC 0300 200 3210. Ive always found the CIS helpline to be really helpful, but they are super rapid issuing fines and dont usually budge on them!
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Joanne
Winner of Bookkeeper of the Year 2015, 2016 & 2017
Thoughts are my own/not to be regarded as official advice,which should be sought from a suitably qualified Accountant.
You should check out answers with reference to the legal position
you were right, (as usual) the tax suffered was correct anyway, and as I had already input the CIS on the HMRC website it didn't have to be on the payroll.
It reconciles with my rec anyway so its all good. Ill be honest I had a mini panic when it wouldn't let me resubmit!