You should be able to see the GST Refund option in the Payments tab in the Taxes menu. Since it's not showing in your QuickBooks Online (QBO), I highly suggest contacting our Phone Support team. They're able to pull up your account in a secure environment and investigate this odd behavior.
Here's how to reach them:
In QBO, click the Help (question mark) icon at the top right.
Select Contact Us at the bottom to connect with our live support.
Just in case, I'll add this article for future reference: