Don't reinstall anything, this is normal. Navigating where things are when you ssh in is a little weird at the beginning until you get used to it.
You can keep metadata with your media folders, but most media servers don't do that. They are generally set up to store the metadata in another area so that when you update the basic program -- emby-server -- you won't destroy your metadata along with the update. Or, really rather, that you can make a back up easily that doesn't get destroyed.
We all dealt with this same issue when getting started. I had to look around the tree to get an idea of where things were stored and it took me a while to understand why it was done that way. It actually does make sense.
The metadata is stored in a slightly different location right now, but you can change it if you prefer.
ETA: So, one simple answer is that if you have metadata (any pictures for your movies, music, etc.), then, yes, it can access the metadata. Don't worry, the paths are built into the program. For me, the metadata is in /var/db/emby-server/metadata which is actually within a much longer full path that includes a path into the jail, then the jail itself, then /var/db/emby-server/metadata
So, all is good. When you set up Emby you decided where to put the metadata, but like most of us you probably didn't pay attention to that step. You could redo the Emby install and see where this occurs if you want, but I would guess that there is a way to either change it now or just accept where it is. It isn't a problem.
Luke or Josh could direct you in the next step if you want to change things, but this is normal.
But one of the most important things you can do with this information (knowing where the metadata is held) is that you can make a copy of it and, if you end up destroying your current jail and if you are happy with the current metadata, you can replace all the metadata by simply replacing the folder created by the new plugin with the one you save.
This matters most if you change any of the metadata. For instance, I don't like the metadata for the Holiday genre in movies, so it saves time for me to save the metadata folder if I destroy the jail for any reason -- and, trust me, I have messed things up enough in the past that I have needed to do that. I also have some music artists and albums that are pretty obscure and not picked up on a general scrape of metadata (audiodb and the like) and so have to add a few images here and there. It helps to have a separate copy of all this info. The other option is to have all of the metadata stored in your media folders (I have done this in the past when using Kodi by exporting the libraries). This can help in loading some of the metadata when you recreate what goes into a plugin, but I think it tends to slow things down.
The easiest way to create a copy of that folder is to ssh in to your freenas box. If you have never done that, probably the easiest way is to download PuTTy or WinSCP (might be easier) and use that to ssh in to your Freenas system. You will need to also go to services in Freenas and turn on ssh (or you won't be able to get in to Freenas). Then you can move around the tree and see where different files are located. I would bet that your emby-server is located along the following path -- /mnt/YourVolume/jails/your jail-name/var/db/emby-server. You could then find the metadata folder and move a copy to your windows computer that you use to ssh in to the Freenas box.
Edited by PhilWhite, 15 August 2017 - 08:09 PM.