CRA indicates that it can treat a late request for a T5013 amendment as a request to assess the partner returns directly

In situations where CRA has not made a determination of partnership income or loss under s. 152(1.4) and the three-year limitation period specified therein has expired, CRA considers that it may only make a determination under s. 152(1.4) where one of the exceptions specified in s. 152(4) applies, e.g., a timely waiver. However, the receipt of a request to amend a T5013 return can be taken into account to assess the returns of the partners directly if they are not statute-barred.

Neal Armstrong. Summary of 17 April 2018 Internal T.I. 2018-0739141I7 under s. 152(1.4).