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. Select Transactions then select the purchase invoice (PI) you want to delete.
2. Select Delete, then press Delete, then press Yes.

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