Please see extract from www.hmrc.gov.uk/employers/doitonline.pdf which explains how to account for the tax free payment your clients received for filing their end of year P35's online.
Accounting for the tax-free payments
Show the tax-free payments in your accounts as 'other operating income'.
The payments are not taxable, so your tax computations should show profit reduced by the payments included in your accounts.
Tax-free payments and VAT
You do not have to pay VAT on your tax-free payments for early online filing, nor do you have to show them on your return.