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I might be misunderstanding you, but here's what I think...
Templates get 'installed' into the database whenever the module is installed or updated via the admin panel. If you've physically added a template file to your module's directory structure and have defined that template file in your xoops_version.php file, then you need to install/update that module from the system admin panel in order to get that template copied into your database.
Also, if you are using a non standard template set, you'll want to ensure that the template set you're using also has the latest copy of the smarty template too.
Hope this helps...