Hello, I remember that in newer versions (in 5.2.9 definitely) there is option to see what file groups will be updated and what will be created. (On EE File Groups, Right mouse click and update file groups and then you see changes before you apply them). I usually rename all current groups to get updates in new fresh groups and in this way I can control also update process. If you update currently existing file groups and they are used somewhere then those updates will applied immediately. If you are missing some options in this update page then you probably didn't install all needed options - just do reinstall once more and select all needed modules/options. And yes I see new client file set called "EEPC52: Endpoint Encryption 5.2.9 Client Files" Hope that helps.
Thanks for that, I ran EEPC setup again & this time left all options as defaults, this time it worked. I must have unchecked something the first time by mistake.