When the CRA reassesses your account and you owe additional GST/HST, you'll want to record that as a tax adjustment and then record the payment.
Here's how you can do it:
Go to All apps, select Sales Tax, then select Overview.
Select Prepare return under the Filings section.
On the Prepare return page, select the Adjust link on the far right of the line you wish to adjust.
Enter the amount of tax you would like to add to the line (to reduce the line, enter a negative number).
Select your adjustment account. This may be an income account for tax credits, or if your Tax Payable account is correct, you can select the Payable account to adjust the return without affecting your Chart of Accounts.
Select Save to save the adjustment.
If you're unsure which adjustment account to use, we recommend consulting with your accountant to ensure the re-assessment amount is classified correctly for your books.