When working with a subcontractor record, you can't allocate a payment on account to an invoice that uses a CIS nominal code. If you've a payment on account to use, you should delete or reverse the payment and then repost it against the relevant invoice.

TIP: If the payment on account has been bank reconciled or, if using VAT Cash Accounting, VAT reconciled you should reverse the transaction. 

[BCB:19:UK - Sales message :ECB]