I have the same issue with a trucking company invoice. And didn't realise it was not recording correct on the HST reports until now i have received a discrepancy letter from CRA. I was recording the sale on the sale receipt and entering a negative for the fuel that was deducted but this is not recording correctly since 2020 which i have NOT REALIZED. Maybe even before but i haven't looked back that far yet. What a nightmare. Did your find a solution?
