What advice should I give in light of the new CDF?

My client has just received a Code of Practice 9 (COP9) notice. I’ve been his adviser for eight years and believe he operates robust accounting systems. A recent VAT visit did not uncover any irregularities though the VAT officer did remove some invoices from the premises. He is adamant however that he has not committed fraud. My client runs a mid-sized incorporated landscaping business and sits on the Board of two local charities. He is concerned that a criminal investigation could ruin his reputation and is considering admitting to deliberate behaviour to get certainty. How should I advise him in light of the June 2014 changes to CDF?