@Deiniol After some thoughts, I agree that removing the Canadian experience would be OK in this case since:
1. In general it is actually better to have Canadian experience in your profile, so removing it from the profile doesn't seem like a mischievous move. In fact, it is hard to think of dishonest motives for why people would remove the Canadian experience from their profile.
2. I imagine that there would be cases in which people actually could've claimed more points but they just forgot about some items, yet still got an ITA, and the omission should be fine, because they are claiming fewer points than they could've claimed (and not the other way around).
3. And yes, you could always write a letter explaining what happens to the the IRCC officer. My suggestion would be to:
a. Take a screen shot of the glitch
b. Write a web form to IRCC and attach the message you wrote them
c. Attach their response to your web form showing that they could not resolve the issue
I think with these three reasons, you are justified to remove the experience and then add it again later.
But I thought once you get an ITA, your profile is locked?