So I used Pacdiff & Meld since it has been awhile and chose to overwrite all the files. To my surprise once this was done and a reboot I found my user was removed from etc/passwd file or the database. So I found a fix for this and wanted to post for anyone who has made this mistake like I have.
Error I would get when I would go to do a eos-update: sudo: you do not exist in the passwd database
I had to add my user back to the ext/passwd file like below. Also I was unable to do this as my user as I could not even log in with my normal user account so I logged into the desktop session as root and then added the below line to the etc/[password file. Sub user name with your own user name and real name with what you used for your real name when you created your user on first install of the OS. I hope this helps anyone who made this same error.
username:x:1000:1000:Real Name,,,:/home/username:/bin/bash
