For those using Klipper, they just released a pretty major change in the way that they store files. When I updated to the latest version all of my config files disappeared. As I looked into it, there seemed to be a lot of other people experiencing the same issue. It turns out that my files did not disappear at all. They were still there, they just had the incorrect file permissions. Here is how I was able to fix it after some Googling.
First, ssh into your pi and take a look in ~/printer_data/config
and ~/klipper_config.
If your files are in one of those places, then you should be fine. If neither of those folders has your config files, then that is a separate issue entirely and you should reinstall moonraker and klipper. If you were able to see the config files in your ssh session, but not from your web access, then run the following commands in ssh.
cd ~/moonraker
git pull
./scripts/data-path-fix.sh