This can be painful to unscramble.  First you have to get to the bottom of the problem in case its the overall sales tax setup that isnt right.  If its just tax codes on items then thats not so bad ...

You then need to deal with the last comment:  I would say the GST/HST Return Report in QBD never filed. - Goto your CRA account and check what has (not) been filed. If you now accidentally miss or duplicate a filing it will make the mess even worse.  Further - for the filings that have been sent to CRA - you need to determine if there have been 'filed in QB' or not.

Once you know the system is working, whats been filed to CRA, and whats been filed in QB,  then the next step is to adjust the QB records to match what has been sent to CRA. That will probably involve a couple of 'sales tax adjustments' - cant detail this now.

Note that the intent is not to 'zero-out' anything, its to make it right - and zero due/refundable is probably not it.