I wanted update the manual way for anyone who needs to fix this in the future.
To run the script file you need to ```
sudo bash ~/RetroPie-Setup/retropie_setup.sh
Once the script runs
1. Manage packages
2. Manage core packages
3. retropie menu
4. update from binary
If your missing the RetroPie-Setup directory, sorry you're going to have to reinstall.
Hope that helps someone!