@Can , Isn’t imposing a stop before Create Invoice in the Order Type not help you in this situation? Then it will not be automatically invoiced.

Also you can check the Invoice Blocked checkbox in the CO line. But you might need some manual intervention here.

Apart from these, nothing comes to my mind other than a custom event which would stop the creation of invoice until fully qty is delivered. 

@Can I believe you can use Backorder Option in Customer Order (defaulted from Customer record) for this purpose.

Ravi correct me if I am wrong, if we use the Backorder option to say for example No Partial Deliveries allowed - it will obstruct the ability to do partial deliveries as well right?. In order to stop the invoicing of partial COs, stopping partial deliveries is too much to ask for I feel.

@Vimukthi Mahakumbura , yes you are correct Vimukthi. I just suggested this for Can to see the possibility of using this in customer’s business. Thanks. 

Thank you for sharing your valuable solution, it's work properly.