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Buy nowGlad to have you here in the Community, @brookermans.
I'm here to ensure you can apply the unapplied payments to your old invoices.
One of the possible reasons why there are unapplied payments is that the invoices were deleted. Let's run the Audit trail report to verify. Here's how:
If the missing invoices were deleted, you have to recreate them and link the unapplied payments. To link them, you can follow the detailed steps provided by my colleague GlinetteC above.
If the invoices weren't deleted, you want to run the Customers & Receivables report. This way, we can verify if the payments were just unapplied.
Just in case you encounter a difference in the A/R balance in the Chart of Accounts and A/R balance on reports, feel free to check out this article for more details: AR balance on the Chart of Accounts does not match AR balance on reports.
Keep in touch if you need any more assistance with this, or there's something else I can do for you. I've got your back. Have a good day.