A different situation, but my spouse (PR) was having this (for a different underlying reason, but similarly something 10 yrs + ago and no longer relevant). Officers also said there's a flag and there's nothing they could do).
We wrote to our MP and explained the situation, and also asked/made the point that this was a waste of resources, etc, as well as a serious burden on us when travelling, all that stuff.
We had to sign a release form and provide some small addl info. Several weeks later they got back and said they'd contacted CBSA (? I think) who gave a cryptic response saying they'd [removed the old flag]* but secondary inspection was always possible, no guarantees, etc. Spouse has not been sent to secondary since then, no issues at all, in several trips.
A few notes: they didn't outright say they'd 'removed the flag' but some convoluted language (don't remember exactly how it was phrased) that I interpret to mean exactly this; no-one ever reacted to my language or denied there are flags or anything like that, which implied to me that our understanding was exactly right. And, the 'no guarantees you could get secondary inspection at any time' is just standard bureaucratic language so of course means nothing.
Finally: my MP's office is pretty good in general and it's a serving senior Minister, I don't know that the inquiry from them had to go to CBSA or if that was where they thought they had more pull. In other words, I let them do their thing and it worked - but MP's offices and staff vary in quality and knowledge of how to work things and of course they act a bit quicker in response to Minister's requests. Good luck.