I have added entry manually and also imported from Bank. Both have matched, now discrepancy difference showing as I have deleted reconciled entry, how to correct ?

I'm here to ensure you'll be able to correct the discrepancy, @accounts-zentree.

Let's start with checking your opening and beginning balances. We have to ensure that they are correctly entered. 

Once done, let's verify that the ending balance you've input is accurate. If you still see a difference,  you have to combine multiple transactions into a single transaction in QuickBooks Online (QBO), if your bank combines several payments as a single record. 

If this does not work, let's proceed in eliminating transactions you know are correct by comparing transactions in your bank statement to the ones entered in QBO.

However, if the issue persists, I'd recommend following Steps 5 to 7 of this article: Fix issues at the end of reconciliation in QuickBooks Online. This also includes links on how you can check your bank statement to see if there are any mistakes.

For your reference in reconciling in QBO, feel free to visit our Reconciliation Hub. 

You can also pull up a Reconciliation report to get a copy of your previous reconciliation and use this as a reference to avoid errors in the future. 

If you have any other concerns about fixing discrepancies in QBO, don't hesitate to leave a reply below. I'd be happy to assist you further. Have a good one.