Unless the uncollected tax on shipping is material, I would start charging the GST/HST on the freight going forward.
You can always file an amended GST/HST return to report the uncollected tax if the missed amount is however material. Section 224 of the Excise Tax Act allows you to go after the customer and even sue them to recover the missed tax once you do report the uncollected tax on an amended GST/HST return, and make the remittance. It is more common practice to remit the missed amount out of your own profit and be done with it.
Right of supplier to sue for tax remitted
http://laws-lois.justice.gc.ca/eng/acts ... ml#docCont