In LEPTON 2.0.0 we started a new system to handle customized template files of modules.
As the modified addon template files were overwritten during upgrade process of modules we now use the /frontend directory in the frontend template also for all addons, that have template files, for example news module.
Copy now the template files of the specified module (here news) in a directory called 'news' within the 'frontend' directory of your template and customize your files. Now the template files ( file.lte) of this addon will not be overwritten by upgrade process of the news module.
This will work with any other module the same way.
Examples can be found in the LEPTON template that is delivered with LEPTON package.