If the torrents are still seeding when the import in arrs happens, it would copy the file(s) to your media folder so you’d have two copies now. If the torrent is done seeding and, I think if you have completed download handling enabled, it’ll do a move instead so you’d end up with only one copy.

Ideally though you want a hardlink compatible setup but from what you said you do not.

Jellyfin just monitors your media folder which is managed by the arrs.

I have no guidance on your issue but just to make sure, this is two commands and not one:

docker exec -it jellyfin ldconfig

sudo systemctl restart docker

Do you get the restarting message with just the first command?

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My understanding is windows does have hardlinks but has a limitation on the amount. Hardlinks link to the same data on the disk, so deleting one just deletes the link but not the data, if you delete all links then the data is deleted. You should have 2 links, one in torrents and one in media. I highly recommend trash guides for setup

The best setup uses hardlinks. Qbit downloads to your torrents directory, when it finishes downloading it tells the arrs which hardlink it during the import to your media folder and jellyfin sees it there. Hardlinks don’t take up extra space but allow you to keep seeding the original while also having a nice renamed media library. Your media folder and torrents folder should never be the same.