templates will be override if they are not customized, installing in master style means install in all styles and you can check for updated templates by using Updated Templates function.
ok but since this is an upgrader script and so and so already has these templates installed as custom templates not in the master style, will this overwrite those custom templates not in the master style?
no, it will not overwrite the custom templates, but you can ask users to do so buy check for updated templates and then revert. or simply remove those templates first and then insert the new ones.
no, it will not overwrite the custom templates, but you can ask users to do so buy check for updated templates and then revert. or simply remove those templates first and then insert the new ones.