Duplicates when moving files

[windowsdan]

To maybe make it a bit clearer. I possibly want to watch something that could be as big as 80gb. I can extract that on my system drive to another folder on my system drive very quickly (m.2 nvme) and I have that folder setup as a location in my JellyFin library. This is so I can go straight to the Shield and watch it immediately. If I wait to copy that size file to a mechanical disk, I'm sitting around for another 20-30 minutes before watching it. However, this is no where I want the files in the long term so I have a script that runs each night to move those files, based on folder, to the mechanical ... into a matching folder.

For example I have on the system drive:
/media/4kdv, /media/4khdr, etc..
On the mechanical:
/mnt/drive/4kdv, /mnt/drive/4khdr, etc..
The 4kdv library would then contain both /media/4kdv and /mnt/drive/4kdv

No folders are ever deleted only the files inside the folders are moved from system drive to hdd. When this happens I get the library metadata for the moved file in the new location and still have the metadata for the old file on the system drive as though I have two copies of the title in the same library but in two different places. The full artwork and metadata shows for the title on the system drive, even though the folder is empty, so obviously if I click play on that version there is an error saying it can't playback.