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.
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