Since a .PUP file is only a container, like a .rar or .zip, it is deleted after it gets installed. (ps3 copies it to HDD, extracts and installs it, then deletes it).
I have found the .PUP file with file manager before. I think when automatic updates are enabled, it downloads it and keeps it in dev_hdd0\tmp\ maybe (can't remember exactly where it was).
But like they said already, you could copy all the dev_flash files, and get coreos by making a dump of the Flash.