Generally speaking, there are very few files in Construct that you'll ever need to edit. The files not affected by upgrades are safe to edit without worry of loosing your customizations when upgrading.
Files not affected by upgrades
Adding your unique look via a custom style sheet or layout override is the best way to customize Construct. Any custom style sheet and extended template overrides will NOT be affected by an upgrade. Generally speaking, any file that you add to the
/css directory and sub-directories are safe.
Starting with Joomla! 1.6, custom core overrides that differ from those provided by Construct, should be created by use of Joomla's native Alternative Layout Feature.
Files affected by upgrades
Files other than the ones that you add to the
/html directory and sub-directories, will be overwritten by an upgrade.
For example, some users may wish to customize Construct's core CSS. If you do so, it will be overwritten and you will loose your customization. In this case, you should leverage the cascade and create a custom declaration that overrides Construct's core style declaration.
Any files that you change should be backed up before upgrading, if you choose to upgrade. After the upgrade is complete, your backed up files can be restored into the new version of Construct, or differences merged.