Hi there, accoounting,

Some data aren't converted when migrating from QuickBooks Desktop (QBDT) to Online. This could be the reason payments were unlinked in QuickBooks Online (QBO).

You can refer to this article: What to expect when you switch from QuickBooks Desktop to QuickBooks Online to know what data doesn't convert during the migration process.

You'll need to manually apply those payments to invoices. Here's how:

1. Click + New.
2. Select Receive Payment under Customers.
3. Enter the name of the customer to open customer invoices and outstanding credits.
4. Add the payment date.
5. Mark the invoice under Outstanding Transactions and the payment under Credits.
6. Click Save and close.

I'm also adding the The QuickBooks Guide to Converting QuickBooks Desktop to QuickBooks Online link for step-by-step guidance, visuals, tips, and hyperlinks in the conversion process.

Let me know if you have follow-up questions, and I'm always around to help you out.