Don't see why you'd approach like this, 'if all else fails' - involving your MP / contacting your MP is your choice and your right.
Not only that, it's good for MPs to know that dumb stuff like this happens, and that it is almost impossible and/or very time consuming and tedious to get it fixed directly. You/we want MPs to pressure immigration to do things better.
True but it's an admin issue. Also some MPs can take months to respond to these type of issues.
I believe I have this resolved now. I reached out to CBSA and CIC/IRCC through various channels. I wrote an email stating that I am now a citizen, provided my passport number, citizenship certificate number and UCI/Client ID. I explained that each time I enter Canada I am sent to secondary to assess the PR Residence Obligation, which makes no sense as I'm now a citizen.
I'll detail what worked for me and also what I tried that didn't work in the hope that it can help someone else.
What worked:
On the 12th of April I emailed
IRCC.CitizenshipConvocation-ConvocationCitoyennete.IRCC@cic.gc.ca, I got this email address from my request to appear for an interview prior to being granted citizenship. They responded to me on the 8th of May, the email came directly from an agent, not a group mail box and said:
"This is to confirm that the alerts in your file have been expired and you should no longer have similar issues.
However, should you continue experiencing problems, you can complete the Canada Border Services Agency (CBSA) Feedback Form:
I also contacts CBSA via their web form
https://www.cbsa-asfc.gc.ca/contact/com-eng.html and submitted a complaint on the 6th of April. They responded on the 9th of May and said:
"This is in response to your message of April 6, 2023, regarding secondary referrals you have been experiencing upon entry to Canada.
The Canada Border Services Agency’s (CBSA) mandate is to ensure that only admissible people and goods enter Canada.
The CBSA has reviewed your file and identified the cause of these referrals. We are pleased to confirm that the information that caused the referrals has now been removed. There are no current flags associated to your name.
While secondary processing may seem an inconvenience to travellers, it is an important part of the normal border process to ensure the safety of all Canadians. As such, all travellers may be subject to examination any time they enter Canada.
Thank you for contacting the Canada Border Services Agency."
I suspect only the first item was required and when CBSA looked at their request they saw that IRCC had already fixed it.
What did not work:
I tried calling CIC/IRCC many times. It took 5 minutes to get through the phone menus only to be told they were too busy to take my call. I even tried this as soon as they opened and at various times of the day. Total waste of time.
I contacted an internal mailbox that CBSA agents can use when someone at the border complains about flags on their file. I found them email address in the CBSA manual here:
https://meurrensonimmigration.com/removing-flags-at-the-port-of-entry/. I got a prompt reply saying this email box was for internal use only and I should submit a query via the CBSA web form.
I emailed
CIC-CITOY-CONVO@cic.gc.ca and received a prompt email telling me this mail box is only for queries relating to the virtual Citizenship Ceremony, and then a few days later an email telling me to phone CIC.
I filled out the IRCC contact form on the 12th of April, I got the following response on the 7th of May:
"Since your question is related to a subject for which we are unable to assist you, we invite you to communicate with the appropriate department in order to obtain the answers to your questions.
Further, the Canada Border Services Agency (CBSA) ensures Canada's security and prosperity by facilitating and overseeing international travel and trade across Canada's border.
For more information, we invite you to visit their website."
The other thing I was planning to do was to print out my GCMS notes which shows the alert, and also print out the section of the CBSA manual above to show to CBSA next time I was sent to secondary screening.
I have yet to test this out by making an entry, but the two messages from CBSA and CIC saying its resolved gives me confidence. Hope that helps someone else.