Mistakes happen, and it's understandable. When creating invoices, you can make as many changes as you want without any repercussions.
But if you've already entered the payment on that invoice (marked as 'Paid'), you will be able to edit the quantity to the invoice. However, this step involves you taking notes of the implications to your accounting integrations.
Go into Sales Orders > Invoices > and click on the respective paid invoice you want to edit.
This step involves first deleting the existing payment on your accounting software.
Thereafter, your updated invoice will be synced with QuickBooks Commerce.