Canada HST method has changed, invoices now incorrect

Everything re taxes used to work perfectly for Canadian HST at different rates for different provinces. Now I have an invoice which was fully paid and I recorded the full payment BUT the invoice said that the customer still owed the taxes of $382! However this is UNTRUE! Why and how did it change and can I get the old method back which worked at least until early 2018.

Nothing has changed with respect to how invoices, with or without tax, are paid recently. You have not given enough information to resolve your difficulty. Can you post screen shots showing (a) the invoice’s edit screen and (b) the receipt by which you recorded the customer’s payment? Obscure proprietary information if necessary, but show the complete line items.