Any file that comes with the Joomla installation is a Joomla "Core" file, not including the files in the included front end templates.. When you upgrade Joomla to a new version, the "Core" files are replaced with the newer versions. If you made edits to the old core files, you will lose your edits.

What you should do is create "overrides" for the core files and make your edits in these override files, not in the core files. These overrides have to be placed in the proper sub-folder of your default template for Joomla to find them and use them. 

What is an override?

When Joomla's php compiles your content and settings to create your web page, it uses a combination of different .php files for instructions on how to put together the HTML document for the browser to display. When pulling up these files, it looks in set locations in your site's directory structure. It will first look to see if you have override files in the html directory of your default template, if there is nothing there, it will go look in the standard locations.

Click here to read the bj.zemplate article on: Creating Overrides

Even if you upgrade your Joomla installation and your template, these overrides will remain unchanged. There can be issues with big jumps in Joomla versions, like from 2.5 to 3+, so you may still need to replace the override file with an updated version with similar edits.

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