CRA indicates that a non-resident registered under the E-Commerce provisions can follow the ETA s. 232 refund procedure if the resident recipient demonstrates that it was registered

Where a non-resident supplier who is registered for GST/HST purposes under the “Electronic Commerce” rather than regular rules and charges GST/HST to a Canadian recipient who has not provided it with evidence that it is itself registered under the regular provisions, CRA considers that if the recipient subsequently provides satisfactory evidence to the non-resident supplier that it in fact was so registered at the time of the supply, then the non-resident can follow the procedures in ETA s. 232(1) for refunding on a timely basis the GST/HST that it charged the Canadian recipient and claim a corresponding credit.

CRA further noted that where a supplier has difficulties in issuing a credit note, the recipient is permitted to issue a debit note to the supplier, containing the prescribed information so as to satisfy the s. 232(3) documentary requirements.

Neal Armstrong. Summary of 14 February 2024 GST/HST Interpretation 231621 under ETA s. 211.17(2)(b).