In our Enterprise environment we do not generally permit local administrative rights to users. When a new version of Desktop Sync is available, a pop-up occurs notifying the user that they can download the new client, but our users cannot install it by themselves. Therefore, it's better for us for admins to be notified of new Desktop Sync versions, and then deploy them to our users. The prompt to upgrade should be suppressed for end users, or at least an option to set that when installing/upgrading.
Actually, we already have a way for you to suppress these updates for users. If you navigate to the Applications tab of the Configuration section of your account's settings, you should see an option to "Notify users of Desktop Sync software updates" (see below). Make sure this option is disabled, and you should be good to go.
Thanks for your question and continued support of Egnyte!