The IR35 legislation is unaffected by the new regime and there is no double charge. Where the company is caught by IR35 and is treated as having made a deemed payment, the deemed payment (and the employers NI) is deductible against the companys profits for corporation tax purposes.
Where a company is treated as making a deemed payment and it makes a distribution in the same or subsequent tax year, it can claim relief in order to avoid a double charge to tax on the individual and the company. Relief is given by setting the amount of the deemed payment against the relevant distribution. This reduces the distribution that is taxable on the individual and the amount of the distribution taken into account for the purposes of calculating the companys corporation tax liability.