Anyway when I ran the auto update I got this message when it did the file check:
New conflicting files
The following files are new within the latest version but it has been determined that there is already a file with the same name within the same position. This file will be overwritten by the new file.
Now to me that doesn't make much sense because those files are not new, they are already existing files. Anyway there was a huge list of files that it wanted to over right. Whatever happened to where it asks you if you want to merge existing code? I did not have that option. Well I went ahead and overwrote the files then I just re installed my mod edits to those files. (Talk about a pain) I would have rather been dragged through an open field of broken glass naked. So after I did all the mod edits I uploaded the files. All my mods are now back intact but I still get the same message and same list of files when I run the file check. So I clicked on the link "show differences" I went through every file that was in question and all that was different was my added code for the mods I have installed. I don't understand why the updater is behaving this way. Any other time it just asks if you want to merge the code.