When I edit an existing shortcut the changes are not applied. Only newly logged on users get the edited/updated shortcuts.

This is by design. The user for which the shortcut has been made available needs to log out and log in again to have the new settings applied. Shortcuts are removed and placed during user login.

Additionally you can configure only managed shortcuts (shortcuts added by Easy Software Deployment). To do this follow these steps:

From the Manager console go to Settings > Shortcuts

Select either or both options to have all personal shortcuts deleted at user login. Be careful though, shortcuts can’t be restored after configuring this feature!