Hell no, My downloads folder in my media folder are completely different. I copy everything from downloads to media It gets renamed, possibly resampled. The torrents are left in the original folder to seed unmolested.

Every once in a while I go through my torrent list and just tell the client to destroy the torrent and files for anything that I don’t care to seed anymore. Zero chance of it breaking my actual store.

Hard links are a built-in feature of basically every modern filesystem. The bigger question to me is, why aren’t hard links working for you?

Yes - but I have no idea about docker, sorry. Have it running baremetal (or rather, in a proxmox VM).

Just a hunch, but in case you “only” share the directory where Sonarr puts Episode files with Jellyfin via some mount point or whatever, and not the directory where Sonarr gets them from (where the torrent client downloads to), then I can see hardlinks breaking in unexpected ways

services:
  gluetun:
    image: qmcgaw/gluetun
    container_name: gluetun
    cap_add:
      - NET_ADMIN
    environment:
      - DNS_ADDRESS=
      - PUID=1000
      - PGID=1000
      - SERVER_CITIES=
      - FIREWALL_VPN_INPUT_PORTS=
      - TZ=Etc/UTC
      # Provider readmes: https://github.com/qdm12/gluetun-wiki/tree/main/setup/providers
      - VPN_SERVICE_PROVIDER=
      #- VPN_TYPE=openvpn
      #- OPENVPN_CUSTOM_CONFIG=/config/custom.conf
      #- VPN_TYPE=wireguard
      #- WIREGUARD_PRIVATE_KEY=
      #- WIREGUARD_ADDRESSES=
    ports:
      - 6767:6767       # bazaar
      - 7878:7878       # radaar
      - 8118:8118       # privoxy
      - 8191:8191       # flaresolverr
      - 8787:8787       # readaar
      - 8989:8989       # sonaar
      - 9091:9091       # transmission
      - 9696:9696       # prowlarr
      # You can add an forwarded listening ports your VPN provider might have here as well.
    volumes:
      - /data/gluetun:/config
  bazarr:
    image: lscr.io/linuxserver/bazarr:latest
    container_name: bazarr
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=Etc/UTC
    volumes:
      - /data/bazarr:/config
      - /share/downloads/movies:/share/downloads/movies
      - /share/downloads/tv:/share/downloads/tv
    restart: unless-stopped
    network_mode: service:gluetun
  flaresolverr:
    # DockerHub mirror flaresolverr/flaresolverr:latest
    image: ghcr.io/flaresolverr/flaresolverr:latest
    container_name: flaresolverr
    environment:
      - LOG_LEVEL=info
      - LOG_HTML=false
      - CAPTCHA_SOLVER=none
      - TZ=Etc/UTC
    restart: unless-stopped
    network_mode: service:gluetun
  privoxy:
    image: caligari/privoxy:latest
    container_name: privoxy
    restart: unless-stopped
    network_mode: service:gluetun
  prowlarr:
    image: lscr.io/linuxserver/prowlarr:latest
    container_name: prowlarr
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=Etc/UTC
    volumes:
      - /data/prowlarr:/config
    restart: unless-stopped
    network_mode: service:gluetun
  radarr:
    image: lscr.io/linuxserver/radarr:latest
    container_name: radarr
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=Etc/UTC
    volumes:
      - /data/radarr:/config
      - /share/downloads/movies:/share/downloads/movies
    restart: unless-stopped
    network_mode: service:gluetun
  readarr:
    image: lscr.io/linuxserver/readarr:develop
    container_name: readarr
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=Etc/UTC
    volumes:
      - /data/readarr:/config
      - /share/downloads/books:/share/downloads/books
    restart: unless-stopped
    network_mode: service:gluetun
  sonarr:
    image: lscr.io/linuxserver/sonarr:latest
    container_name: sonarr
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=Etc/UTC
    volumes:
      - /data/sonarr:/config
      - /share/downloads/tv:/share/downloads/tv
    restart: unless-stopped
    network_mode: service:gluetun
  transmission:
    image: lscr.io/linuxserver/transmission:latest
    container_name: transmission
    environment:
      - PUID=1000
      - PGID=1000
      - TZ=Etc/UTC
      - TRANSMISSION_WEB_HOME= #optional
      - USER= #optional
      - PASS= #optional
      - WHITELIST= #optional
      - PEERPORT= #optional
      - HOST_WHITELIST= #optional
    volumes:
      - /data/transmission:/config
      - /share/downloads/movies:/share/downloads/movies
      - /share/downloads/books:/share/downloads/books
      - /share/downloads/tv:/share/downloads/tv
    restart: unless-stopped
    network_mode: service:gluetun
  watchtower:
    container_name: watchtower
    image: containrrr/watchtower
    volumes:
      - /var/run/docker.sock:/var/run/docker.sock
    network_mode: service:gluetun

You might also want to check out https://yams.media/, it’s pretty much an install script and configuration walkthrough that’s very complete and detailed. Includes most relevant Arrs and gluetun builtin. Containerized. Choice of Emby, Plex or Jellyfin.