Greetings, Nasir. 

I appreciate the detailed reply and giving the exact error messages. I'll take it from here and ensure you'll be able to sync your Shopify data. 

The Invalid Reference Id error (Line.SalesItemLineDetail.ItemRef and Accounts element id 65) suggests that there is an inactivated item or account. 

Did you do the purge by inactivating those products or accounts? In this case, make sure to reactivate those non-duplicated items and accounts. A few of them might still be inactive, which is why you're getting those errors. 

Here's how to do it: 

Reactivate products or services:

1. Go to the Gear icon menu, then select Products and services.
2. Click the Filter button.
3. Set the Status to Inactive.
4. Click Apply. 
5. Check those items with the (deleted) tag, then click Make active. 

Reactivate accounts: 

1. Go to Accounting, then go to the Chart of Accounts tab.
2. Click the small gear icon right above the Action column.
3. Check Include inactive.
4. Review the accounts and compare them with your Shopify mapping. 
5. Click the Make active button on the inactive accounts.

If you've completely purged your company, then this might be related to your sync settings in your Shopify account.

I would recommend checking it and see what's causing the errors. You'll want to contact Shopify's support if you need help with this. 

If you also need to connect your bank account to match or categorize your transactions, you can check this article for a guide: Connect bank and credit card accounts to QuickBooks Online. 

I'm here to help if you have more questions about syncing your data in QuickBooks Online. If you have any other concerns, please add them to your reply.