When uninstalling a Windows Installer application you may run into a scenario where files to be removed may or may not be in use and locked. During the uninstall Restart Manager will show a dialog prompting the user to either stop the locking process or allow the machine to be rebooted at the end of the install. A situation is possible where files will have been deleted or updated as requested by Windows Installer but you do not see the reboot prompt at the end of the install.
There is no harm in making any of the choices offered by Restart Manager. Although a reboot would normally be required if the processes are not stopped, no such reboot will be required or offered. The dialogs are misleading and can be confusing.