@ametz1201 

"So the money that was received into the undeposited funds just sat there and still is. So now all payments received into my bank name from the drop down menu not undeposited funds. So I have large negative QBO balance showing and large amount sitting in undeposited funds when looking at the chart of accounts."

I'm confused by your comment about having a large negative balance.  What account has a negative balance?  Is it the same negative balance as the positive balance from the duplicate transactions in UF?  If so, this should be an easy fix.  If not, read on. 

Please re-read my very first post.  You need to look at the entries sitting in Undeposited Funds (UF) and confirm that they are all duplicates and, if they are, then they need to be reversed since it sounds like these transactions are pre-2023. 

The bigger issue here is that this is double-entry accounting and every entry hits two accounts.  So, if you received a payment and it's sitting in UF, then that same amount is sitting in another account and you need to reverse the entry to that account as well. 

Run a balance sheet report.  Under Other Current Assets, you will see Undeposited Funds.  Click on the amount listed to the right.  That will pull up a transaction report.  Click 'Switch to classic view'.  Make sure the dates of the report go back far enough to include the open transactions.  Find the open transactions.  Look under the SPLIT column.  That is the other account that is being affected.   

To reverse the transactions sitting in UF, you can create an expense transaction (New > Expense), choose Undeposited Funds from the Payment account drop-down and under Category and amount, choose the same category and amount as the duplicate transactions.  That will reverse the duplicate entries sitting in UF.