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I can see how this situation impacts your task, especially in processing reconciliation. No worries, we'll sort this out!
You can create a large deposit and drop one line down. Then enter the income account with a negative amount of the total deposit to clear the funds. Doing this makes your net deposit become zero.
Here’s how:
It would be best to contact your accountant to assist you further with this process.
I've attached an article that helps ensure books are balanced and accurate: Learn the reconcile workflow in QuickBooks. It has everything you need to start a new reconciliation, fix balance issues, and make changes.
Please know that I appreciate all your effort in trying to resolve these old undeposited funds issue and for reaching out to our support for help. You can leave a message on this thread if you have any other questions or concerns about managing your company file. The Community is always here to help. Keep safe always!