That's probably what they'll do. "Not a meal replacement but sold in convenient 2000kcal pouches... wink wink".
I don't know about CFIA, but CRA (Canada Revenue Agency) can and does punish violations of the spirit of the law. That is, if a company finds a loophole that allows them to avoid taxes without violating the letter of the law, CRA is legally allowed to prosecute them anyway for violating the spirit of the law. It is not unlikely that such common sense discretions are given to CFIA as well.
This is almost certainly about false claims/marketing based on usage of regulated industry terms. Simply removing the offending labeling would bring them into compliance.