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you WANT your custom templates to be overwritten on module update? Trust me, in 95% of these cases, that is the last thing you want, since all your changes will be lost.
If you have to update the templates because it is a new version of the module with changes to the templates, rendering your custom ones useless, you should go to System Admin -> Templates -> [Template set name] -> [module] -> delete the affected templates
Then afterwards, press "regenerate" to insert the default template in the custom template set.