With Perfex you have ability to edit all the files located on application/views without editing the core files so in this case you wont need to worry the updates except if any huge changes made in the files.
Ex. if you want to edit the dashboard of the admin area.
Go to application/views/admin/home.php and copy this file after that rename it to my_home.php. Now the content will be taken from my_home.php file not from home.php
You can repeat this steps for all files located in application/views/
NOTE: If you use this feature make sure you re-check your my_ files after upgrade in case any big changes in the file. If you are getting blank pages try reverting to the original file to check if the my_ file cause the issue.