I was surprised to get a quick response from AS about it. I will get a new certificate for companion fare with 90-day validity from the time of issue.
At least they informed you about the 90 day expiration. I had to cancel a flight with a companion fare attached. They told me it would be reissued, but the agent did not mention once that it would have an expiration of 90 days from reissue. I made the (wrong) assumption that it would retain the original expiration of June 2021. Went to book a flight with it 93 days later and poof, it was gone.
.......And that's when I canceled my AS card.