Uninstalling jellyfin on truenas scale

[Efficient_Good_5784]

It made sense that mine would be borked, but i have no idea how to set it back to point to jellyfins FFMPEG directory or if there is a conflict that I can change. I found "ffmpeg-6.0-essentials" in a directory and deleted it.

Making a new container will bring with it the correct FFMPEG used by Jellyfin. No setup required and it will point to it automatically.
Maybe try making a new container instead of using ix-system's auto-update for the container?

Barring that, if I uninstall from truenas scale will I lose all of my configs, databases and settings when I reinstall?

You will lose any files that are not externally mounted since you're dealing with containers. As the name implies, things inside of it are contained and kept separate from the rest of the host system.
If you have not made any steps to make a dataset specifically for Jellyfin's config folder and host mounted that config folder dataset to the container, you have the config folder inside the container.

Basically, the Jellyfin config folder contains all your settings and metadata. You can simply do the following:

1. Make a new dataset, then add it as a host mount to your current Jellyfin container.
   
2. Go to the container/app's shell (found in the app's GUI box), then copy and paste the config folder from the container into the new dataset.
   
3. Once done, you can now link the config folder found in the new dataset to any new Jellyfin containers/apps that you will launch.