With the Sage 50 Accounts CIS v2 module, you can correct and refund subcontractor payments, even after submitting a CIS Return. 

To check if you're using the CIS v2 module:

1. Go to Help then select About.
2. Under Features Enabled, check that CIS v2 shows Yes.

Select the correction you need to make:

Delete an unpaid CIS purchase invoice

Fully refund a CIS invoice and payment

Delete a CIS purchase payment - Standard VAT

Edit CIS payment details