Jellyfin doesnt laucnh after server restart

[EpicRG]

Hey,
My entire server suddenly crashed("due to full main harddrive").
After i restarted the system and fixed the storage issue(just by extending a drive partition) Jellyfin wasn't willing to start at all.
I run jellyfin via docker
Can i fix this without having to reinstall the docker container?

Here are the logs from the docker container:

[19:29:42] [INF] [1] Main: Jellyfin version: 10.10.7
[19:29:42] [INF] [1] Main: Environment Variables: ["[JELLYFIN_CACHE_DIR, /config/cache]", "[JELLYFIN_LOG_DIR, /config/log]", "[JELLYFIN_DATA_DIR, /config/data]", "[JELLYFIN_CONFIG_DIR, /config]", "[JELLYFIN_WEB_DIR, /usr/share/jellyfin/web]"]
[19:29:42] [INF] [1] Main: Arguments: ["/usr/lib/jellyfin/bin/jellyfin.dll", "--ffmpeg=/usr/lib/jellyfin-ffmpeg/ffmpeg"]
[19:29:42] [INF] [1] Main: Operating system: Ubuntu 24.04.2 LTS
[19:29:42] [INF] [1] Main: Architecture: X64
[19:29:42] [INF] [1] Main: 64-Bit Process: True
[19:29:42] [INF] [1] Main: User Interactive: True
[19:29:42] [INF] [1] Main: Processor count: 8
[19:29:42] [INF] [1] Main: Program data path: /config/data
[19:29:42] [INF] [1] Main: Log directory path: /config/log
[19:29:42] [INF] [1] Main: Config directory path: /config
[19:29:42] [INF] [1] Main: Cache path: /config/cache
[19:29:42] [INF] [1] Main: Temp directory path: /tmp/jellyfin
[19:29:42] [INF] [1] Main: Web resources path: /usr/share/jellyfin/web
[19:29:42] [INF] [1] Main: Application directory: /usr/lib/jellyfin/bin/
[19:29:42] [FTL] [1] Main: Unhandled Exception
System.InvalidOperationException: There is an error in XML document (0, 0).
---> System.Xml.XmlException: Root element is missing.
  at System.Xml.XmlTextReaderImpl.Throw(Exception e)
  at System.Xml.XmlTextReaderImpl.ThrowWithoutLineInfo(String res)
  at System.Xml.XmlTextReaderImpl.ParseDocumentContent()
  at System.Xml.XmlReader.MoveToContent()
  at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderMigrationOptions.Read4_MigrationOptions()
  at System.RuntimeMethodHandle.InvokeMethod(Object target, Void** arguments, Signature sig, Boolean isConstructor)
  at System.Reflection.MethodBaseInvoker.InvokeWithNoArgs(Object obj, BindingFlags invokeAttr)
  --- End of inner exception stack trace ---
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromStream(Type type, Stream stream)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromFile(Type type, String file)
  at Jellyfin.Server.Migrations.MigrationRunner.RunPreStartup(ServerApplicationPaths appPaths, ILoggerFactory loggerFactory)
  at Jellyfin.Server.Program.StartApp(StartupOptions options)
  at Jellyfin.Server.Program.<Main>(String[] args)
Unhandled exception. System.InvalidOperationException: There is an error in XML document (0, 0).
---> System.Xml.XmlException: Root element is missing.
  at System.Xml.XmlTextReaderImpl.Throw(Exception e)
  at System.Xml.XmlTextReaderImpl.ThrowWithoutLineInfo(String res)
  at System.Xml.XmlTextReaderImpl.ParseDocumentContent()
  at System.Xml.XmlReader.MoveToContent()
  at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderMigrationOptions.Read4_MigrationOptions()
  at System.RuntimeMethodHandle.InvokeMethod(Object target, Void** arguments, Signature sig, Boolean isConstructor)
  at System.Reflection.MethodBaseInvoker.InvokeWithNoArgs(Object obj, BindingFlags invokeAttr)
  --- End of inner exception stack trace ---
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromStream(Type type, Stream stream)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromFile(Type type, String file)
  at Jellyfin.Server.Migrations.MigrationRunner.RunPreStartup(ServerApplicationPaths appPaths, ILoggerFactory loggerFactory)
  at Jellyfin.Server.Program.StartApp(StartupOptions options)
  at Jellyfin.Server.Program.<Main>(String[] args)
[19:29:43] [INF] [1] Main: Jellyfin version: 10.10.7
[19:29:43] [INF] [1] Main: Environment Variables: ["[JELLYFIN_WEB_DIR, /usr/share/jellyfin/web]", "[JELLYFIN_CACHE_DIR, /config/cache]", "[JELLYFIN_LOG_DIR, /config/log]", "[JELLYFIN_DATA_DIR, /config/data]", "[JELLYFIN_CONFIG_DIR, /config]"]
[19:29:43] [INF] [1] Main: Arguments: ["/usr/lib/jellyfin/bin/jellyfin.dll", "--ffmpeg=/usr/lib/jellyfin-ffmpeg/ffmpeg"]
[19:29:43] [INF] [1] Main: Operating system: Ubuntu 24.04.2 LTS
[19:29:43] [INF] [1] Main: Architecture: X64
[19:29:43] [INF] [1] Main: 64-Bit Process: True
[19:29:43] [INF] [1] Main: User Interactive: True
[19:29:43] [INF] [1] Main: Processor count: 8
[19:29:43] [INF] [1] Main: Program data path: /config/data
[19:29:43] [INF] [1] Main: Log directory path: /config/log
[19:29:44] [INF] [1] Main: Config directory path: /config
[19:29:44] [INF] [1] Main: Cache path: /config/cache
[19:29:44] [INF] [1] Main: Temp directory path: /tmp/jellyfin
[19:29:44] [INF] [1] Main: Web resources path: /usr/share/jellyfin/web
[19:29:44] [INF] [1] Main: Application directory: /usr/lib/jellyfin/bin/
[19:29:44] [FTL] [1] Main: Unhandled Exception
System.InvalidOperationException: There is an error in XML document (0, 0).
---> System.Xml.XmlException: Root element is missing.
  at System.Xml.XmlTextReaderImpl.Throw(Exception e)
  at System.Xml.XmlTextReaderImpl.ThrowWithoutLineInfo(String res)
  at System.Xml.XmlTextReaderImpl.ParseDocumentContent()
  at System.Xml.XmlReader.MoveToContent()
  at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderMigrationOptions.Read4_MigrationOptions()
  at System.RuntimeMethodHandle.InvokeMethod(Object target, Void** arguments, Signature sig, Boolean isConstructor)
  at System.Reflection.MethodBaseInvoker.InvokeWithNoArgs(Object obj, BindingFlags invokeAttr)
  --- End of inner exception stack trace ---
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromStream(Type type, Stream stream)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromFile(Type type, String file)
  at Jellyfin.Server.Migrations.MigrationRunner.RunPreStartup(ServerApplicationPaths appPaths, ILoggerFactory loggerFactory)
  at Jellyfin.Server.Program.StartApp(StartupOptions options)
  at Jellyfin.Server.Program.<Main>(String[] args)
Unhandled exception. System.InvalidOperationException: There is an error in XML document (0, 0).
---> System.Xml.XmlException: Root element is missing.
  at System.Xml.XmlTextReaderImpl.Throw(Exception e)
  at System.Xml.XmlTextReaderImpl.ThrowWithoutLineInfo(String res)
  at System.Xml.XmlTextReaderImpl.ParseDocumentContent()
  at System.Xml.XmlReader.MoveToContent()
  at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderMigrationOptions.Read4_MigrationOptions()
  at System.RuntimeMethodHandle.InvokeMethod(Object target, Void** arguments, Signature sig, Boolean isConstructor)
  at System.Reflection.MethodBaseInvoker.InvokeWithNoArgs(Object obj, BindingFlags invokeAttr)
  --- End of inner exception stack trace ---
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
  at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromStream(Type type, Stream stream)
  at Emby.Server.Implementations.Serialization.MyXmlSerializer.DeserializeFromFile(Type type, String file)
  at Jellyfin.Server.Migrations.MigrationRunner.RunPreStartup(ServerApplicationPaths appPaths, ILoggerFactory loggerFactory)
  at Jellyfin.Server.Program.StartApp(StartupOptions options)
  at Jellyfin.Server.Program.<Main>(String[] args)

[EpicRG]

Update, found the solution:

In my case, I stopped the docker container.
Then i navigated to where the config files were stored on my system. I found it through portainer, but you can also find it in your docker compose file.
Then i renamed the files migrations.xml and system.xml to migrations.xml.bak and system.xml.bak
After that i restarted the container and that resolved my issue

Hopes this helps anyone