If the intermediary carries out work for a client before 6 April 2000 but is paid in arrears after 6 April 2000 will this affect the end of year turnover figure in the accounts?

The effect of the new legislation is to create a notional deemed payment on which an amount of tax and NICs has to be paid. It does not affect the turnover of the company nor how its income should be represented in the accounts, which is determined by established accounting principles. If you have any questions about the basis used for the preparation of your accounts you should contact your professional adviser.