Fix multiple version handling

MediaBrowser.Controller/Entities/BaseItem.cs

@@ -1430,10 +1430,15 @@ namespace MediaBrowser.Controller.Entities
                 });
                 foreach (var removedExtra in removedExtras)
                 {
-                    LibraryManager.DeleteItem(removedExtra, new DeleteOptions()
+                    // Only delete items that are actual extras (have ExtraType set)
+                    // Items with OwnerId but no ExtraType might be alternate versions, not extras
+                    if (removedExtra.ExtraType.HasValue)
                     {
-                        DeleteFileLocation = false
-                    });
+                        LibraryManager.DeleteItem(removedExtra, new DeleteOptions()
+                        {
+                            DeleteFileLocation = false
+                        });
+                    }
                 }
             }
 

MediaBrowser.Controller/Entities/Movies/Movie.cs

@@ -9,8 +9,10 @@ using System.Text.Json.Serialization;
 using System.Threading;
 using System.Threading.Tasks;
 using Jellyfin.Data.Enums;
+using MediaBrowser.Controller.Library;
 using MediaBrowser.Controller.Providers;
 using MediaBrowser.Model.Entities;
+using Microsoft.Extensions.Logging;
 
 namespace MediaBrowser.Controller.Entities.Movies
 {
@@ -91,6 +93,20 @@ namespace MediaBrowser.Controller.Entities.Movies
             };
 
             var id = LibraryManager.GetNewItemId(path, typeof(Movie));
+
+            // Check if the file still exists
+            if (!FileSystem.FileExists(path))
+            {
+                // File was removed - clean up any orphaned database entry
+                if (LibraryManager.GetItemById(id) is Movie orphanedMovie && orphanedMovie.OwnerId.Equals(Id))
+                {
+                    Logger.LogInformation("Alternate version file no longer exists, removing orphaned item: {Path}", path);
+                    LibraryManager.DeleteItem(orphanedMovie, new DeleteOptions { DeleteFileLocation = false });
+                }
+
+                return;
+            }
+
             if (LibraryManager.GetItemById(id) is not Movie movie)
             {
                 movie = LibraryManager.ResolvePath(FileSystem.GetFileSystemInfo(path)) as Movie;
@@ -109,6 +125,9 @@ namespace MediaBrowser.Controller.Entities.Movies
             }
 
             await RefreshMetadataForOwnedItem(movie, copyTitleMetadata, newOptions, cancellationToken).ConfigureAwait(false);
+
+            // Create LinkedChild entry for this local alternate version
+            LibraryManager.UpsertLinkedChild(Id, movie.Id, LinkedChildType.LocalAlternateVersion);
         }
 
         /// <inheritdoc />

MediaBrowser.Controller/Entities/Video.cs

@@ -19,6 +19,7 @@ using MediaBrowser.Model.Dto;
 using MediaBrowser.Model.Entities;
 using MediaBrowser.Model.IO;
 using MediaBrowser.Model.MediaInfo;
+using Microsoft.Extensions.Logging;
 
 namespace MediaBrowser.Controller.Entities
 {
@@ -428,6 +429,17 @@ namespace MediaBrowser.Controller.Entities
         {
             var hasChanges = await base.RefreshedOwnedItems(options, fileSystemChildren, cancellationToken).ConfigureAwait(false);
 
+            // Clean up LocalAlternateVersions - remove paths that no longer exist
+            if (LocalAlternateVersions.Length > 0)
+            {
+                var validPaths = LocalAlternateVersions.Where(FileSystem.FileExists).ToArray();
+                if (validPaths.Length != LocalAlternateVersions.Length)
+                {
+                    LocalAlternateVersions = validPaths;
+                    hasChanges = true;
+                }
+            }
+
             if (IsStacked)
             {
                 var tasks = AdditionalParts
@@ -467,7 +479,21 @@ namespace MediaBrowser.Controller.Entities
                 SearchResult = null
             };
 
-            var id = LibraryManager.GetNewItemId(path, typeof(Video));
+            var id = LibraryManager.GetNewItemId(path, GetType());
+
+            // Check if the file still exists
+            if (!FileSystem.FileExists(path))
+            {
+                // File was removed - clean up any orphaned database entry
+                if (LibraryManager.GetItemById(id) is Video orphanedVideo && orphanedVideo.OwnerId.Equals(Id))
+                {
+                    Logger.LogInformation("Owned video file no longer exists, removing orphaned item: {Path}", path);
+                    LibraryManager.DeleteItem(orphanedVideo, new DeleteOptions { DeleteFileLocation = false });
+                }
+
+                return;
+            }
+
             if (LibraryManager.GetItemById(id) is not Video video)
             {
                 video = LibraryManager.ResolvePath(FileSystem.GetFileSystemInfo(path)) as Video;
@@ -486,6 +512,11 @@ namespace MediaBrowser.Controller.Entities
             }
 
             await RefreshMetadataForOwnedItem(video, copyTitleMetadata, newOptions, cancellationToken).ConfigureAwait(false);
+
+            // Create LinkedChild entry for this local alternate version
+            // This ensures the relationship exists in the database even if the alternate version
+            // was created after the primary video was first saved
+            LibraryManager.UpsertLinkedChild(Id, video.Id, LinkedChildType.LocalAlternateVersion);
         }
 
         private void RefreshLinkedAlternateVersions()

MediaBrowser.Controller/Library/ILibraryManager.cs

@@ -20,6 +20,7 @@ using MediaBrowser.Model.IO;
 using MediaBrowser.Model.Querying;
 using Episode = MediaBrowser.Controller.Entities.TV.Episode;
 using Genre = MediaBrowser.Controller.Entities.Genre;
+using LinkedChildType = MediaBrowser.Controller.Entities.LinkedChildType;
 using Person = MediaBrowser.Controller.Entities.Person;
 
 namespace MediaBrowser.Controller.Library
@@ -229,6 +230,14 @@ namespace MediaBrowser.Controller.Library
         /// <returns>Enumerable of linked Video items.</returns>
         IEnumerable<Video> GetLinkedAlternateVersions(Video video);
 
+        /// <summary>
+        /// Creates or updates a LinkedChild entry linking a parent to a child item.
+        /// </summary>
+        /// <param name="parentId">The parent item ID.</param>
+        /// <param name="childId">The child item ID.</param>
+        /// <param name="childType">The type of linked child relationship.</param>
+        void UpsertLinkedChild(Guid parentId, Guid childId, LinkedChildType childType);
+
         /// <summary>
         /// Adds the parts.
         /// </summary>

MediaBrowser.Controller/Persistence/IItemRepository.cs

@@ -12,6 +12,7 @@ using MediaBrowser.Controller.Entities;
 using MediaBrowser.Controller.Entities.Audio;
 using MediaBrowser.Model.Dto;
 using MediaBrowser.Model.Querying;
+using LinkedChildType = MediaBrowser.Controller.Entities.LinkedChildType;
 
 namespace MediaBrowser.Controller.Persistence;
 
@@ -234,4 +235,13 @@ public interface IItemRepository
     /// <param name="toChildId">The child ID to re-route to.</param>
     /// <returns>Number of references updated.</returns>
     int RerouteLinkedChildren(Guid fromChildId, Guid toChildId);
+
+    /// <summary>
+    /// Creates or updates a LinkedChild entry linking a parent to a child item.
+    /// If the link already exists, updates the child type.
+    /// </summary>
+    /// <param name="parentId">The parent item ID.</param>
+    /// <param name="childId">The child item ID.</param>
+    /// <param name="childType">The type of linked child relationship.</param>
+    void UpsertLinkedChild(Guid parentId, Guid childId, LinkedChildType childType);
 }