Having the same issue here but on QBDT. So far what I am doing is pulling a report on the CGS GST and moving it to the ITC's via JE since that is where they should be going in the first place. I am going to continue playing around with sales tax codes and see if I can link a new code on cost of sales. 

There are so many instances where it is necessary to have deductions appear on invoices such as referral fees and many examples in the agriculture industry (cattle sale deductions, grain sale deductions, consignment fees for equipment etc)