This 'phoning home' occurs every time the game is launched, and is independent of patches. Steam's 'phone-home' capability has been known to override only some elements of a mod, producing mixed results for no apparent reason.
As a consequence, every time a patch to the game is released, or Steam 'verifies' the game files, any such mods will be removed when the original (or 'vanilla') version of the files are restored, and eventually you will find it necessary to reapply many, if not all of your desired mods. Some mod changes have to be made by altering the hex code of the game executable file (.exe) directly, or by replacing original game files.
