Let's say I need an alternative layout of an administrator module. So I copy the file of the module from the administrator/modules/my_module/tmpl/default.php and put it inside administrator/templates/isis/html/my_module/default.php.
And here is my question: Am I going to loose this created folder/file on Joomla's update since isis is default Joomla's administrator template?
You will be safe. The "Isis" administrator template layouts do not get updated when the core of Joomla! is updated. Technically, the template is not part of the core code.
To verify the update date of a template, you would typically look at the details of the template in Extensions > Templates > Templates. For Administrator templates, you would select "Administrator" as the type. You will see the "Version" is "1.0" and the "Date" is "3/30/2012" for Isis. However, for this template, the date and version are inaccurate as the Joomla! team has not accurately documented their updates.
Important: With all customizations that you make, always keep a backup locally in case something happens (of course, you should be keeping a backup of the entire site, anyway).
