This can be achieved, but you'll have to re-enter the line information on the invoice you're wanting to credit to maintain the amount on that invoice - which you can then apply a credit too.
Click on the invoice you want to credit, click on one linked transaction in top left and then remove on the estimate. You'll at this point need to manually re-add the information back into the invoice that the system has automatically removed when unlinking the estimate.
This will put the balance of the estimate back to (eg) £900.
You can then create a credit note and link it against the invoice in question using the Receive Payment function on the invoice, thereby writing that invoice off.
You can then re-issue the invoice as required based on the estimates new remaining balance.