Server crashed on SQL access

[Idanr]

I'm running jellyfin in a docker environment on my OMV server. I've let my server run out of storage which I assume caused the issue. The server became unavailable, and after restarting it started complaining about invalid XML file (0,0) during migration. I've deleted migrations.xml and tried again, but this time got an SQL error.
I've tried deleting all the db files - jellyfin, library, library-journal, and migrations.xml again, and no dice. Jellyfin creates the again on restart and showes the same issue. 
Here is the issue from the log:

Code:

[ERR] [1] Jellyfin.Server.Migrations.MigrationRunner: Could not apply migration 'MigrateActivityLogDatabase'
CannotOpen: SQLitePCL.pretty.SQLiteException: unable to open database file
  at SQLitePCL.pretty.SQLiteException.Throw(Int32 rc, Int32 extended, String msg)
  at SQLitePCL.pretty.SQLiteException.CheckOk(sqlite3 db, Int32 rc)
  at SQLitePCL.pretty.SQLiteDatabaseConnectionBuilder.Build()
  at Jellyfin.Server.Migrations.Routines.MigrateActivityLogDb.Perform()
  at Jellyfin.Server.Migrations.MigrationRunner.PerformMigrations(IMigrationRoutine[] migrations, MigrationOptions migrationOptions, Action`1 saveConfiguration, ILogger logger)
[19:54:48] [FTL] [1] Main: Error while starting server.
CannotOpen: SQLitePCL.pretty.SQLiteException: unable to open database file
  at SQLitePCL.pretty.SQLiteException.Throw(Int32 rc, Int32 extended, String msg)
  at SQLitePCL.pretty.SQLiteException.CheckOk(sqlite3 db, Int32 rc)
  at SQLitePCL.pretty.SQLiteDatabaseConnectionBuilder.Build()
  at Jellyfin.Server.Migrations.Routines.MigrateActivityLogDb.Perform()
  at Jellyfin.Server.Migrations.MigrationRunner.PerformMigrations(IMigrationRoutine[] migrations, MigrationOptions migrationOptions, Action`1 saveConfiguration, ILogger logger)
  at Jellyfin.Server.Migrations.MigrationRunner.Run(CoreAppHost host, ILoggerFactory loggerFactory)
  at Jellyfin.Server.Program.StartApp(StartupOptions options)
[19:54:48] [INF] [1] Main: Running query planner optimizations in the database... This might take a while
[19:54:48] [INF] [1] Emby.Server.Implementations.ApplicationHost: Disposing CoreAppHost
[19:54:48] [INF] [1] Emby.Server.Implementations.ApplicationHost: Disposing SchedulesDirect
[19:54:48] [INF] [1] Emby.Server.Implementations.ApplicationHost: Disposing MusicBrainzAlbumProvider
[19:54:48] [INF] [1] Emby.Server.Implementations.ApplicationHost: Disposing EmbyTV
[19:54:48] [INF] [2] Main: Received a SIGTERM signal, shutting down
[19:54:50] [INF] [1] Main: Jellyfin version: 10.8.10

[TheDreadPirate]

At this point I would move, not delete, the entire jellyfin config directory and start from scratch. Who knows what was corrupted when it ran out of storage. There could be a lot more partially written files than just the DB files.