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Hi I am one of the experts. Tax year is from 6 Apr 18 to 5 Apr 19 as you know already, so if vis vouchers are missing then contact your contractor and get all info. Or call HMRC Cis helpline and ask them how much cis is deducted at source. Normally HMRC takes some time to send you the letter but you can try. I would only put cis tax that is deducted for sure and you have got evidence in hand because in any way HMRC has got an actual record and in case wrong info is submitted then you should expect inspection.
Hope I have answered your question?
This tax year is from 6 apr 2018 to 5 apr 2019 so please put relevant earnings and expenses to this tax period. This info from 1/9/17 to 5/4/2018 belongs to your 2017/18 tax return. Is that clear now?