Generally speaking WordPress will update the .htaccess file any time you change the permalink structure. Many plugins will also update/modify the file as needed.
But the default structure of the .htaccess file allows you to lay it out in such a way that WordPress will not overwrite your custom entries.
WordPress will overwrite the entries between ‘# BEGIN WordPress’ and ‘# END WordPress’. While most plugins will create their own begin and end tags and only update within those tags.
Simply put your custom entries outside of any custom tags/comments and they SHOULD be preserved when WP updates the file.