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.
I now must admit to a different problem - I have tried to unsubscribe from notifications on this thread several times, and I cannot. Can anyone from Airmail or Tenderapp remove me from notifications? I ended up using a different email client that allowed for searchable archives, so I don't need updates here anymore.