I do not see how upgrading our application would have anything to do with some type of custom thing you have running elsewhere.
Just my thoughts
If you are using for instance the inc_features.php script in our application to do that it by nature is suppose to show here on the forumhome Ford Explorer Ranger Enthusiasts "Serious Explorations"®
So really this means if your using our scripting to do it you have altered it. My suggestion would be to NOT upload the inc_features.php file
Other than that you must upload everything except the 2 config files and maybe that inc_features.php file and run the required upgrades.