MIgration from ubuntu server (portainer) to unraid (docker compose)

[Jalle914]

Hello everyone,

I am trying to migrate my current jellyfin server from portainer (ubuntu) to unraid (docker compose manager).

I have read a lot of posts here and guides and it seems so straight forward but something in my data is not working as I was hoping it would do.

Mapstructure in portainer (Ubuntu):

/docker/jellyfin
├── config
│   ├── branding.xml
│   ├── encoding.xml
│   ├── logging.default.json
│   ├── metadata.xml
│   ├── migrations.xml
│   ├── network.xml
│   ├── system.xml
│   └── users
├── data
│   ├── collections
│   ├── device.txt
│   ├── introskipper
│   ├── jellyfin.db
│   ├── jellyfin.db-shm
│   ├── jellyfin.db-wal
│   ├── keyframes
│   ├── kodisyncqueue.db
│   ├── kodisyncqueue-log.db
│   ├── library.db
│   ├── library.db-shm
│   ├── library.db-wal
│   ├── playlists
│   ├── ScheduledTasks
│   ├── splashscreen.png
│   └── subtitles
├── log
│   ├── FFmpeg.DirectStream-2025-08-01_22-01-15_a38e6bb53350d53b98b28139dab7eef7_073042c3.log
├── metadata
│   ├── artists
│   ├── library
│   ├── People
│   ├── Studio
│   └── views
├── plugins
│   ├── configurations
│   ├── InPlayerEpisodePreview_1.3.1.0
│   ├── Intro Skipper_1.10.10.17
│   ├── Kodi Sync Queue_14.0.0.0
│   ├── TheTVDB_19.0.0.0
│   ├── TMDb Box Sets_11.0.0.0
│   └── Trakt_26.0.0.0
├── root
│   └── default
└── stats
    ├── backup-data
    └── postgres

Mapstructure in unraid (docker compose manager):

/mnt/cache/appdata/jellyfin
├── cache
│  ├── images
│  ├── omdb
│  └── transcodes
├── data
│  ├── data
│  ├── metadata
│  ├── plugins
│  ├── root
│  └── transcodes
├── encoding.xml
├── log
│  ├── FFmpeg.DirectStream-2025-08-04_20-06-38_d56066345cca280c36724f6709e7c17a_525d1fc2.log
│  ├── FFmpeg.DirectStream-2025-08-04_20-09-34_52af40c802a77ba8c115f24c19b25dee_3e0c8aa0.log
│  ├── FFmpeg.DirectStream-2025-08-04_20-11-51_d0c778a3088dbe2fe8cb6eeddeb04433_7cea71a7.log
│  ├── FFmpeg.Transcode-2025-08-04_20-11-51_d0c778a3088dbe2fe8cb6eeddeb04433_81ed9eb1.log
│  ├── FFmpeg.Transcode-2025-08-04_20-11-51_d0c778a3088dbe2fe8cb6eeddeb04433_ff4d6fc9.log
│  └── log_20250804.log
├── logging.default.json
├── migrations.xml
├── network.xml
└── system.xml


They are a bit different but I did my best and I only needed the library.db and jellyfin.db. When moved and server is booted, the users are there and saved media as well (Currently watching, next up etc.)

What I cannot do however is link my media drive to my movies and shows folder. My docker compose is the following:
services:
  jellyfin:
    image: lscr.io/linuxserver/jellyfin:latest
    container_name: jellyfin
    environment:
      - PUID=99
      - PGID=100
      - TZ=Europe/Oslo
    volumes:
      - /mnt/user/appdata/jellyfinconfig
      - /mnt/disks/D7JPS3HN/datamedia
    devices:
      - /dev/dridev/dri 
    ports:
      - 8096:8096
      - 7359:7359/udp #Service Discovery
      - 1900:1900/udp #Client Discovery
    restart: unless-stopped

My error when trying to link my media is showing following:

[2025-08-04 18:36:55.728 +02:00] [ERR] [20] MediaBrowser.Controller.Entities.BaseItem: Error refreshing owned items for "/config/root/default/Movies"
System.IO.DirectoryNotFoundException: Could not find a part of the path '/config/root/default/Movies'.
  ...
[2025-08-04 18:36:55.728 +02:00] [ERR] [21] MediaBrowser.Controller.Entities.BaseItem: Error refreshing owned items for "/config/root/default/Shows"
System.IO.DirectoryNotFoundException: Could not find a part of the path '/config/root/default/Shows'.

Why is it showing this? And how can I fix it? I want my data kept when migrating as much as possible..