Go to the prepayment and un-check the invoice to which the payment was applied and then save.

I’ve tried that--there is a check box but it will not let me uncheck it.

You need to reset, then delete the deposit for that payment, then you can delete the payment and re-enter it correctly. When you recreate the deposit, it will resend it to your accounting system (Quickbooks) so you will need to delete the duplicate deposit in QB.