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

Delete an unpaid CIS purchase invoice

1. Click Transactions then click the purchase invoice (PI) you want to delete.
2. Click Delete, then click Delete, then click Yes.

The system deletes the invoice or, if you're on the Standard VAT scheme and its VAT reconciled, reverses it with further postings.