Hi there, TrendyGroup.
Creating a standalone invoice will leave half of your estimate open. You can delete that invoice, and create one from the estimate instead.
On the other hand, I think you’re referring to the invoice payment about your reconciliation. You can leave it as it is. The payment will just be converted as credits when you delete your invoice. From there, you can apply it back when you create a new one from the estimate.
After you have done the steps, I'd suggest printing and sending the invoice again to check if you still get the same behavior.
I'll be around if you need more help with getting rid of these errors.