If you don't agree with a CRA assessment, you should contact CRA.  They will know why there is a 10% difference between what you calculated, and what was refunded.

I agree with Randy.  The CRA will know why there is a difference, but the reporting assessment should have indicated something.  If they took a long time to send it to you there will be interest owing applied that you need to record as revenue.

As for why those accounts are zero now?  If you think about the logic of what you are trying to do, it will be easier to understand.  First, you record sales and purchases.  The sales amount of sales tax is trust money you hold for the CRA.  That is showing up in the liabilities (probably Acct 2310) of the balance sheet.  That is because liabilities track what you owe.  You owe that money to the CRA.

The sales tax on purchases are allowed to reduce the amount you charged for GST and HST.  So those amounts show on the balance sheet as a negative to affect or reduce the amount you owe (Acct 2315).

When you record an amount owing or refund, it will reduce those amounts to zero because you no longer owe the money (or the CRA no longer owes you).  If you never posted an entry to Adjustments and Refund or have already accounted for those amounts in your remittance entry, then they will be zero also.

This of course assumes you have posted the remittance amount on the last day of the period (I do).

Hope this helps

I am surprised that they didn't request a reason for the difference.  They usually give you 20 days to explain the difference especially if they are the one coughing up more money.

Now it makes sence. ! Thank you.