Hello mrhillan,
Once you set up the customer profile as a CIS contractor, QuickBooks will calculate the CIS deductions automatically.
We'll need to update the customer profile to stop QuickBooks from calculating CIS deductions. Here's how:
Future invoices of the said customer will no longer be calculated for CIS deductions. You can can click here to know more about it.
You can always get back to us if you have more questions.