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Payments
Thanks for getting back into this thread and providing details of what you've done so far, @bengw1218. Let me lay out some information regarding your concern about handling unapplied credits in QuickBooks Online (QBO).
One of the possible reasons that it still showed up in your Accounts Payable (A/P) Detail report after paying/linking them is that the date of the Journal Entry is not the same as the date on your credits.
To sort this out, you can update the Journal date to the same date as the credits by pulling up the A/P detail report. Here's a sample screenshot for your visual reference:
To make sure that the correct credit and journal entry are linked properly, we can use the expense or check option instead of the pay bills window.
If the issue persists, can you please share a screenshot of how it showed up in your A/P Aging Detail report? And how did you link the credit to the journal entry?
Additionally, you can customize your vendor reports in QBO to show the correct data for each company. Then, you can use this resource as a reference if you want to export your reports to Excel: Export your reports to Excel from QuickBooks Online.
I'd love to know how it goes after performing the steps above, as I want to ensure this is resolved for you. Just leave a comment below, and I'll get back to you. Goodbye for now, and have a great day ahead!