Thanks for reaching out in the Community. I'll be happy to assist you by sharing more info on this.
QuickBooks Online offers automation features, including to automatically apply credits to an invoice. This might mark your invoices as paid upon creation. If this feature is on, here's how you can turn it off:
Select the Gear icon
Click Account and Settings
Select Advanced
Select Pencil icon in Automation
Remove the check-mark in the box next to Automatically apply credits
If you're using QuickBooks Online Payments, call our phone support team at 1-855-253-1536 so they can look into this further. Our agents are available Monday to Friday, 9 a.m. to 8 p.m. and Saturday from 9 a.m. to 6 p.m.
Let me know if you have any other questions.
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