How to do a silent update?

Hi, I’m a sysadmin for a school and I’m already silently deploying Arduino 1.6.13, with the 2 drivers, on the student’s computers. What I’m trying to figure out is a way to bypass the popup when I try to an update on a computer where an older version of Arduino is already present? The popup ask if I want to remove, can’t remember exactly, the user projects or something. So my question is how to a silent update? I simply want to install the latest version of the application in my labs.

Thanks in advance for the help!
Guillaume Boucher