With a subcontractor who is CIS registered, why can you not allocate a credit with a T0 VAT code to an invoice with a T1 VAT code?

We enter applications with the T0 tax code, which are then later credited when we receive the VAT invoice.

So last month I paid an application with the T0 tax code to ensure out VAT return is correct. I have now eventually received the VAT invoice, so have credited the application and entered the VAT invoice with T1 VAT code. I am now left with 2 transactions but cannot make a payment. What would you suggest I do?

I can also not amend any transaction after it has been paid, so cannot change them all to T1 so the VAT return is still correct.

Also on the same theme …. I have a supplier who had one invoice which fell under the CIS scheme as it was commissioning, now every time I want to make a payment, I have to allocate credits to invoices, even if they are not meant to be.