Some one linked the bank account and the bookkeeper was also entering each bank transaction manually. So now we have 2 bank accounts, how can I get rid of the other bank?

Hi there, 

You've come to the right place for help. I'll be happy to share info about deleting a bank account in QuickBooks. 

To disconnect an account:

1.     In the navigation bar, click Banking, and then select the Banking sub-tab.
2.     Select the account you want to delete, and then click on the pencil icon. 
3.     In the Account window, select Disconnect this account on save.
4.     Click on Save and Close.              

Give these steps a try and let me know you make out. I'll be on standby in case you need further assistance. 

Thank You, for the reply.

Problem here is that duplicate bank  account ( Scotia bank operating account ) is showing on my balance sheet but does not show under banking. So how can I delete/ disconnect this account.

I see what you're saying. If the account is showing up on the Balance Sheet, you'd have to make it inactive and I'll show you how. Here are the steps:

1.     Go to Settings ⚙ and select Chart of Accounts.
2.     Find the account you want to hide.
3.     Select the small arrow ▼ in the ACTION column. Then select Make inactive.

To check the accounts you made inactive in the Chart of Accounts tab: Select Settings ⚙ above the Action column, then select Include inactive. 

If you need to make the account active again, follow these steps: 

1.     Go to Settings ⚙ and select Chart of Accounts.
2.     Select Settings ⚙ above the action column. Then select Include inactive.
3.     Find the account you want to use again and select Make active.
    

Give these steps a try and let me know if you're still seeing that account on your Balance Sheet. 

If I inactivate that account, QB will create an adjusting transaction.

Since the account has duplicate transactions, you can delete the transactions or move them to the right account. Let me know if you need help with this.