Hi there, @chelsealmyers.

Thanks for dropping by the Community. Allow me to jump in for a moment and share some information about clearing up old invoices that were paid, but not recorded in QuickBooks Online (QBO).

Since you've converted from QuickBooks Desktop (QBDT) to QBO, it's possible that these were entered as a journal entry (JE). The only piece of information that isn't converted is a JE's billable status; you can't make them billable in QBO. You can check out this article for more information: What data doesn't convert from QuickBooks Desktop to QuickBooks Online?

If that's the case, let's pull up the transaction list by customer report to search for the payments and link them to the open invoices. Here's how:

1. Go to Reports menu at the left pane, then enter transaction list by customer on the search bar.
2. Click the Customize option, then select your preferred date on the General section.
3. On the Rows/Column drop-down, put a checkmark in the Open Balance checkbox.
4. On the Filter drop-down, choose Payments on the Transaction Type.
5. Hit Run report.

Once pull up, click each unapplied payments and link them to their corresponding invoices.

That should point you in the right direction. Please let me know how it goes by leaving a comment on this thread. I'm only a post away if you have any follow-up questions about the process. Have a good one!