The warning is designed to let you know that reducing the quantity on the invoice leaves the Sales Order partially open for the remaining quantity, Jetnjmy.
You can manage your Preferences to turn off one-time warnings and messages if you want to remove it while you work. Follow these steps on how to do it:
- Go to the Edit menu, then select Preferences.
- Click General on the left, then proceed to the My Preferences tab.
- Look for the box that says "Bring back all one-time messages." Then, uncheck it.
- Click OK.

After that, change the quantity ordered or invoiced once again. When the warning appears, look for a checkbox on the warning message itself that says "Do not show this message again", or similar wording, and then check it before clicking OK.
The system will mark it as "Invoiced in Full" and will close it automatically if the number of orders on the Invoice equals the number in the Invoiced column in the Sales Order.

If the quantity on the Invoice is less than the quantity on the Sales Order, QuickBooks assumes that you will invoice the remaining balance later. This is why it's not automatically closed. However, you can manually change the status of the Sales Order to close it out. Just open the transaction and put a checkmark under the CLSD column.

I checked the release notes for the most recent QuickBooks Desktop updates, and they do not indicate any changes to the Sales Order functionality.
You can find the detailed articles on the latest updates here:
Lastly, can you share a screenshot of the Sales Order that shows a Balance Due? We just want to make sure that we're giving you the right information for the third question.
Feel free to reply to this thread to share additional details or a screenshot of the Sales Order. You can also visit us anytime you have other questions for us.