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?