How to replace the existing part template with new part template ?

You can disable the existing template under Site > Templates and then create new templates that refer to your updated parts.

Alternatively, if you create the majority of your CAD data within Creo, you can store your start parts as CAD Documents within Windchill and then set your config.pro options to point to them. These start parts can be updated as normal CAD Documents. Templates are mainly used if you use the Create New CAD Document wizard to create your CAD data within the workspace.

Refer to the Using Creo with Windchill guide (starting on p. 108) for information on how to set the pro_*_dir and template_* config.pro options to point to your Windchill environment.