CRA generally will accept a late ETA s. 156 substantively-available election if the parties have been treating themselves as subject to it

When asked when it will accept a late-filed ETA s. 156 nil consideration election (on form RC4616), CRA responded:

CRA normally accepts these when the registrant is eligible, compliant and there is some sort of evidence that the registrant has been applying these rules consistently. This evidence could be a note in the file that says election GST25 [the former s. 156 election form] in use.

Neal Armstrong. Summary of May 2017 Alberta CPA Roundtable, GST/HST Q.5 under ETA s. 156(4)(b)(ii).