When using the AeXAgentUtil.exe /clean parameter, it can have an adverse affect on your computer, but this depends on where you installed the agent. Once you run the AeXAgentUtil.exe /clean, it will go through its folder and all subfolders deleting files. So placing the agent on the Root of the computer, Program Files, Windows, or any folder that has files you don't need deleted, causing the agent to delete these files.
ITMS 7.x, 8.x
Installing the agent to its default folder or in its own subfolder, where only Altiris files are installed. A change has been implemented so that if the user chooses to install to the root of the drive or to the "Program Files" directory, the installer will append an "Altiris" subdirectory to the path so the agent is not installed directly to the root or Program Files directory. Please use caution when using or recommending the use of the /clean switch. It will delete all files and subdirectories under the directory where the agent is installed. Also, if the agent was previously installed in another location and later removed, it is possible that the /clean switch will delete everything in the previous install location as well.
All clients where you have installed the Altiris agent.