Manual Upload File Uploaded Amounts Incorrectly

I'm not sure why you're trying to download the old data?  Assuming you've been Reconciling your account monthly, QBs will ignore all of the downloaded info as the transactions are already Reconciled.  The Bank Feed will only sync with items that have not already been cleared by a prior Bank Feed or have been reconciled.

The Bank Feed is to match and confirm there are no errors in what you've entered into your Register and what the bank actually added or withdrew from your account.  It makes the Reconciliation process a lot faster if you're checking the transactions throughout the month and know that they are correct when you close out the month.

Hello, 

The problem is that it hasn't been reconciled monthly. We had not data from April 2021- September 2021. When I re-synced the account at the end of this year it only pulled transactions from the last 3 months, there were no transactions from April- September, which is why I manually uploaded the transactions from my bank. 

Thanks for getting back to us, redfoxhauling.

To get this sorted out, you can use the Exclude feature in QuickBooks Online and delete the incorrect transactions. Here are the steps to complete the process:

1. Click Transactions in the left panel and choose Banking.
2. Select the connected bank account.
3. From the For Review tab, select all the incorrect transactions.
4. Tap on the Exclude button.
   
5. Go to the Excluded tab, select the transactions again.
6. Hit the Delete button.
   

After that, you can follow the steps in the following article to import and label them correctly: Manually upload transactions into QuickBooks Online. On the same write-up, you'll find links on how to set up bank rules as well as reconciling your account.

Once imported, I recommend editing, assigning, and categorizing your transactions. Also, you can match them to the existing entries in the software. Doing so will help you ensure the accuracy of your financial records.

Please know that I'm just a post away should you need anything else. I'm always here to help and ensure that your questions are addressed accordingly. Wishing you a wonderful week ahead.

In addition to what @Rose-A said...  Be sure to go back to your monthly bank statements and Reconcile each month.  It will REALLY help keep things in order and make sure that all the bank records are in order. 

(My guess is your Tax Accountant is also going to want to know if the accounts are Reconciled.)