Movie Library Contents have disappeared after updating

[otherjustin]

Last night I updated to 10.11.1. Got everything working correctly and then I started a transfer of content to multiple libraries. Everything seems to have worked fine except for my Movies library, as I noticed this morning the new additions were not shown on Jellyfin despite confirming that the files are in the proper location. I rescanned the library, expecting the movie count shown on the Admin Dashboard to move from 382 to 396. Instead, it now says 27 and the actual Library in Jellyfin shows no content at all (The 27 are likely movies located in other libraries).

I have tried restarting the server and scanning again. A semi-related forum post suggested checking for outdated plugins, but everything I have installed supports at least 10.11 if not 10.11.1. To be safe I just uninstalled all plugins and tried another rescan, but nothing. I have also tried removing the library in Jellyfin and recreating it, but that did not fix the issue either.

The server is running on Debian through docker official.

EDIT: Previous version I updated from was 10.10.7

[otherjustin]

I attempted running a scan of just the problem library, here is the log

[2025-11-01 20:47:02.562 +00:00] [ERR] [64] MediaBrowser.Controller.Entities.BaseItem: Error refreshing owned items for "/media/Media/Movies"
System.IO.IOException: Input/output error : '/media/Media/Movies/Perfect Blue (1997) [BluRay] [1080p] [YTS.AM]'
at System.IO.FileStatus.ThrowOnCacheInitializationError(ReadOnlySpan1 path)
at System.IO.FileSystemInfo.Create(String fullPath, String fileName, Boolean asDirectory, FileStatus& fileStatus)
at System.IO.Enumeration.FileSystemEnumerator1.MoveNext()
at System.Linq.Enumerable.IEnumerableSelectIterator2.ToArray()
at MediaBrowser.Controller.Providers.DirectoryService.<>c.<GetFileSystemEntries>b__5_0(String p, IFileSystem fileSystem)
at System.Collections.Concurrent.ConcurrentDictionary2.GetOrAdd[TArg](TKey key, Func3 valueFactory, TArg factoryArgument)
at MediaBrowser.Controller.Providers.DirectoryService.GetFileSystemEntries(String path)
at MediaBrowser.Controller.Entities.BaseItem.GetFileSystemChildren(IDirectoryService directoryService)
at MediaBrowser.Controller.Entities.BaseItem.RefreshMetadata(MetadataRefreshOptions options, CancellationToken cancellationToken)
[2025-11-01 20:47:02.589 +00:00] [ERR] [64] MediaBrowser.Providers.Folders.FolderMetadataService: Error validating images for "/media/Media/Movies"
System.IO.IOException: Input/output error : '/media/Media/Movies/Perfect Blue (1997) [BluRay] [1080p] [YTS.AM]'
at System.IO.FileStatus.ThrowOnCacheInitializationError(ReadOnlySpan1 path)
at System.IO.FileSystemInfo.Create(String fullPath, String fileName, Boolean asDirectory, FileStatus& fileStatus)
at System.IO.Enumeration.FileSystemEnumerator1.MoveNext()
at System.Linq.Enumerable.IEnumerableSelectIterator2.ToArray()
at MediaBrowser.Controller.Providers.DirectoryService.<>c.<GetFileSystemEntries>b__5_0(String p, IFileSystem fileSystem)
at System.Collections.Concurrent.ConcurrentDictionary2.GetOrAdd[TArg](TKey key, Func3 valueFactory, TArg factoryArgument)
at MediaBrowser.Controller.Providers.DirectoryService.GetFileSystemEntries(String path)
at MediaBrowser.LocalMetadata.Images.LocalImageProvider.GetFiles(BaseItem item, Boolean includeDirectories, IDirectoryService directoryService)
at MediaBrowser.LocalMetadata.Images.LocalImageProvider.GetImages(BaseItem item, IDirectoryService directoryService)
at MediaBrowser.Providers.Manager.ItemImageProvider.<>c__DisplayClass7_0.<ValidateImages>b__0(ILocalImageProvider i)
at System.Linq.Enumerable.SelectManySingleSelectorIterator2.ToList()
at MediaBrowser.Providers.Manager.ItemImageProvider.ValidateImages(BaseItem item, IEnumerable1 providers, ImageRefreshOptions refreshOptions)
at MediaBrowser.Providers.Manager.MetadataService2.RefreshMetadata(BaseItem item, MetadataRefreshOptions refreshOptions, CancellationToken cancellationToken)
[2025-11-01 20:47:02.622 +00:00] [ERR] [64] MediaBrowser.Controller.Entities.BaseItem: Error retrieving children from file system
System.IO.IOException: Input/output error : '/media/Media/Movies/Perfect Blue (1997) [BluRay] [1080p] [YTS.AM]'
at System.IO.FileStatus.ThrowOnCacheInitializationError(ReadOnlySpan1 path)
at System.IO.FileSystemInfo.Create(String fullPath, String fileName, Boolean asDirectory, FileStatus& fileStatus)
at System.IO.Enumeration.FileSystemEnumerator1.MoveNext()
at System.Linq.Enumerable.IEnumerableSelectIterator2.ToArray()
at MediaBrowser.Controller.Providers.DirectoryService.<>c.<GetFileSystemEntries>b__5_0(String p, IFileSystem fileSystem)
at System.Collections.Concurrent.ConcurrentDictionary2.GetOrAdd[TArg](TKey key, Func3 valueFactory, TArg factoryArgument)
at MediaBrowser.Controller.Providers.DirectoryService.GetFileSystemEntries(String path)
at MediaBrowser.Controller.Entities.BaseItem.GetFileSystemChildren(IDirectoryService directoryService)
at MediaBrowser.Controller.Entities.Folder.GetNonCachedChildren(IDirectoryService directoryService)
at MediaBrowser.Controller.Entities.Folder.ValidateChildrenInternal2(IProgress`1 progress, Boolean recursive, Boolean refreshChildMetadata, Boolean allowRemoveRoot, MetadataRefreshOptions refreshOptions, IDirectoryService directoryService, CancellationToken cancellationToken)

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Wait a minute... Perfect Blue isn't even showing up as a file or folder in the directory at all, but that is what's being referenced in the error. Any ideas?

[otherjustin]

Ok update: I shared as much detail in case updating Jellyfin was a red herring, and it was.

While transferring files to the media drive, power was lost and I had to restart. Turns out that caused a corrupted file, and since it is an NTFS drive on a Debian server, I had to dualboot into windows to run chkdisk and fix it, then go back to Debian and everything's good now.