To make your Undeposited Funds balance to zero, you'll have to match and move transactions to the appropriate bank. Rest assured, this process won't cause any double entries in your account. The Undeposited Funds account works as a holding account that's used to hold payments from all of your checking and savings accounts. You can't make this account inactive or deleted.
Here's a couple of Community Articles that can help you with cleaning up your Undeposited Funds:
You never ever ever get paid in person or through the mail? Undeposited Funds is where all of your received payments from paid invoices as well as sales receipts should land. You are supposed to match these to the deposits in the bank feed. The only only only way to duplicate income is to categorize cash flow (bank deposits) as income. Bank deposits are not income - only a record of cash flow- movement of funds from one current asset (undeposited funds) to another (checking account)
Even if you deleted every transaction that ever hits UF you could not delete the account and at best make it inactive but I doubt you can even do that since this is a special account created by the software and if you could make it inactive as soon as your next sale the software would create it again.
Now this does not mean you cannot post a sales receipt payment or other payment directly into banking(never do this when a bank deposit contains more than one check or payment from multiple customers) but you still have to "match". You cannot add the bank feed as income since the sales receipt is your income.