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We can correct how the down payments were recorded. However, we'll need to do it one transactions at time.
Then, you can record the down payments through Receive payments or Bank deposits.
If you select Bank deposit, here's how to affect it to the customer's account:
Then, use the bank deposit as invoice payment. You can use these links for more information:
Record invoice payments in QuickBooks Online
Record and make Bank Deposits in QuickBooks Online
You might also ask your accountant to see if they have a way to correct these details in bulk. They know what's best for you and your books.
Keep us posted if you have additional questions.