So I was totally right on this.
I called in today and inquired this issue. They acknowledged that the issue has been fixed even though the missing points weren't reinstated. To get you missing points reinstated, you will need to open an investigation so the back office can calculate how much they owe you.

It`s very typical CSR practice according to my many years of running several e-commerce business. Companies know they can easily get away with it because most consumers aren't gonna spend time on this.

First, they understood that if they could fix the ongoing issues, then most clients will simply not notice the past missing point.
Second, they probably made projection that instead spending all that manpower and $ to reinstate our points, they could just wait til customers file a missing point investigation. (Probably half of them don't even notice)

So here we are. If you want to get your points back, you should definitely call and ask AMEX to open an investigation on your missing points in April/May. Your missing points will not miraculously shows up in your account because it was probably a calculated decision by AMEX.