The function of the ClientSideClonePrepTool is to clear the SEP Hardware ID on a machine and leave the machine without a hardware ID so that a template or a base image can be created out of that machine. Templates or base images created in such way will not have the Hardware ID and hence every new machines made out of this template will generate a unique hardware ID for itself.
Just to confirm, this tool is NOT to be executed on cloned computers, after being cloned with a SEP hardware ID already present in the template or the base image.
Symantec provides a seperate tool (RepairClonedImage.exe) for clearing Hardware ID from computers on which the hardware ID is already duplicated. This tool can be run silently. Please check the following link for more details on this tool.
http://www.symantec.com/docs/TECH163349