That message means your EXE.XML file was ALREADY corrupted before launching our installer, which is why the installer gave the message about not having touched it.
And, you are not using the current version of the sceneries or the Addon Manager because, the current version, in case your XML files are found to be corrupted, will also ask if you want to create a new, correct, version.
So, just download and install the current version of the sceneries and/or the Addon Manager, and the installer will be able to fix the XML file for you.