If the GST refund comes in lower than the one claimed what steps should I take to clear the difference?

Hi there, 

QuickBooks Online makes it easy to record a GST refund and I'll be happy to show you how. 

If the cause of the difference was a clerical error, you'll need to unfile your taxes and then file again using the correct amounts. To do this, contact our support team using this link here. Otherwise, here's how to record a GST refund:

1. First of all, open your sales tax center by clicking on the Taxes tab. 
2. Make sure you're on the Sales Tax tab and Returns tab (see screenshot). 
3. Find the relevant filing. 
4. Click the option in the Action column (it should be Record Payment). 
5. Select Refund and then fill in the refund information. 
6. Click Save. 

Give this a try and if you have questions, I recommend contacting our payroll support team using this link.