If you edited directly all the files, you will indeed have the same problem with all the other templates and you will indeed have to overwrite your modified files with the ones from the install package in order to restore them.
That's why we strongly recommend to do the changes via the interface. That way, you can easily revert your changes in the future. It might be a bit longer at the beginning if you know your way around, but you'll loose time on such things with updates, conflicts etc where you would have been able to easily revert your changes in a few clicks.