Nope, I made another folder so it would overwrite the vanilla versions and not get deleted by future patches. Naming files with a "_" before the name will make it a first priority to read. so for example you see "CH" make another file that is "_CH" and start placing files in the correct order. Example: _CH -> Accessory or PC -> Your modded files. Its a better way rather than just replacing them every patch.
I tried that route just a few minutes ago as well but for some odd reason none o fthe mods are working. I do know when the patch went in place the launcher wouldn't work anymore and the repair was grayed out. Sounds like I may need to uninstall and get a fresh download in case it's a corrupted file from their update.
Thanks for the heads up on the extra file, I will use that in the future.