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How are you checking the size? Some tools will split file size based on the number of hard links. So a 10GB file may show as 5GB in folder A and the other 5GB in folder B.
Also, if you're using Docker. Its crucial that your downloads and media directories are listed as a single volume. If it's two volumes, it'll copy rather than hard link.
I have a feeling it may just be TrueNAS reporting it weirdly, or at least not in the way I expected.
I've just checked the file system in the console and the folders in question have multiple hard links when I run ls -la.
I think TrueNAS is just marking the qbt download dir's size as the full amount of the folders before they're hard linked. Either way it's recorded I'm sure it's not actually duplicating the data now! phew!
And yes I'm aware of the docker issues, whilst vague radarr/sonarr explained it pretty well
I use Docker for my setup and mistakenly had my qBittorrent download folder and my *arr media folders mounted as /downloads and /movies as opposed to /arr/downloads and /arr/movies
The *arr programs running inside their containers don't know that the two folders are actually on the same drive because it sees them as two separate mount points. Once I changed my *arr containers to mount my directories correctly, the hard linking worked as expected instead of copying files over. I then ran fclones and recovered over 700 GB of storage from deduplication.