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Is there a chance you remembered it wrong or that the school made a mistake in warning you?
Actually, what happened was the school gave me the warning but shortly thereafter a grade change for that semester was processed. The grade change put me over the top. At that point the school must have rescinded the warning (or never recorded it?) but I was never sent anything. I do know that my record is clean and that if my school sends a deans cert-- it will say so.
You should disclose the mistake either way, just in case it comes back to bite you, so you did the right thing there.
I would probably leave well enough alone, but if you want to send them an e-mail describing the situation (“I was told that I was placed on AP, but this was the result of a clerical error/error on reporting of my grades.”), that would be fine too. As you said, the GPA is what’s going to hurt you, not really whether you were on AP because of it.