>> Not sure if this is something new in 6.44 but when I copy my certificate there, it is deleted upon running the web server.
From the release notes;
6.19 (10 February 2012)
Important Change: The setting on the WebServer procedure for secure sites, Certificate, is no longer relative to the web folder, but relative to the app folder. The folder will be moved automatically from "relative to web" to "relative to app".
So your certificates are being moved from app\web\certificates to \app\certificates when the app runs.
cheers
Bruce