If you have replaced all of the GST and PST calculations with HST, you do need to create a new group that has the old configuration. Then just switch the tax group on the header of the credit note.
You can get more information on changing taxes here:
http://www.softrak.com/resources/technicaltips/changingsalestax.phphttp://www.softrak.com/pdf/technicaltips/ChangingTaxRatesinAdagio.pdfI would strongly suggest getting in contact with your Adagio dealer who will be better able to assist you.