Hello, ian-figtreehomes.

I'll be glad to share some information about your situation.

When you invoice a full amount for a specific item, it will not show up on your second invoice. The item that doesn't have a remaining balance will have a Closed status on the estimate. 

I've got these sample screenshots for reference:

To learn more about progress invoicing in QuickBooks, you can read this article: Set up and send progress invoices in QuickBooks Online.

Please let me know if you have more questions related to progress invoicing or other concerns. I'm here to answer them. Have a great day!