I am having the same problem. However, it appears to be intermittent where some archived emails are showing up in Archive and others are not. Also, I am using the alpha version of AirMail 3 and not the beta.
I'm getting the same issue in Airmail 3. But I can find them if I search for them, I just can't figure out where they are being held such that search is finding them. It's not in the Archive folder. This is very concerning. I'd love to use the button to move them to archive but once that happens, they're no longer visible. Would be nice to see a response from the developer on this.