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It’s nice to see you again in the Community, @mikey007.
Deleting the duplicate entries and depositing the rest can help fix the issue. Make sure to link them to your customers’ invoices to avoid having unapplied balances.
Let’s first create a backup for the company file to avoid any accidental data loss. Then, run the Deposit Detail report to delete the duplicate entries.
Once done, deposit the remaining payments. Follow these steps:
Check out this article for the details and screenshots of entering a bank deposit: Record and make Bank Deposits in QuickBooks Desktop.
Reach out to me if you have additional concerns, or need further assistance performing the steps above. It's always a pleasure to help. Have a good one!
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Thanks, this solution looks to be what I need! Thanks for the help.