diff --git a/Emby.Server.Implementations/Library/LibraryManager.cs b/Emby.Server.Implementations/Library/LibraryManager.cs
index 2acfd68c36..830c918541 100644
--- a/Emby.Server.Implementations/Library/LibraryManager.cs
+++ b/Emby.Server.Implementations/Library/LibraryManager.cs
@@ -428,6 +428,9 @@ namespace Emby.Server.Implementations.Library
                     newPrimary.SetPrimaryVersionId(null);
                     newPrimary.UpdateToRepositoryAsync(ItemUpdateType.MetadataEdit, CancellationToken.None).GetAwaiter().GetResult();
 
+                    // Re-route playlist/collection references from deleted primary to new primary
+                    _itemRepository.RerouteLinkedChildren(video.Id, newPrimary.Id);
+
                     // Update remaining alternates to point to new primary
                     foreach (var alternate in alternateVersions.Skip(1))
                     {
@@ -436,6 +439,12 @@ namespace Emby.Server.Implementations.Library
                     }
                 }
             }
+            else if (item is Video alternateVideo && !string.IsNullOrEmpty(alternateVideo.PrimaryVersionId)
+                && Guid.TryParse(alternateVideo.PrimaryVersionId, out var primaryId))
+            {
+                // If deleting an alternate version, re-route references to its primary
+                _itemRepository.RerouteLinkedChildren(alternateVideo.Id, primaryId);
+            }
 
             var children = item.IsFolder
                 ? ((Folder)item).GetRecursiveChildren(false)
@@ -3480,5 +3489,11 @@ namespace Emby.Server.Implementations.Library
             _fileSystem.CreateShortcut(lnk, _appHost.ReverseVirtualPath(path));
             RemoveContentTypeOverrides(path);
         }
+
+        /// <inheritdoc />
+        public int RerouteLinkedChildReferences(Guid fromChildId, Guid toChildId)
+        {
+            return _itemRepository.RerouteLinkedChildren(fromChildId, toChildId);
+        }
     }
 }
diff --git a/Jellyfin.Api/Controllers/VideosController.cs b/Jellyfin.Api/Controllers/VideosController.cs
index 2237e36b5f..1c8b695458 100644
--- a/Jellyfin.Api/Controllers/VideosController.cs
+++ b/Jellyfin.Api/Controllers/VideosController.cs
@@ -222,6 +222,9 @@ public class VideosController : BaseJellyfinApiController
 
             await item.UpdateToRepositoryAsync(ItemUpdateType.MetadataEdit, CancellationToken.None).ConfigureAwait(false);
 
+            // Re-route any playlist/collection references from this item to the primary
+            _libraryManager.RerouteLinkedChildReferences(item.Id, primaryVersion.Id);
+
             if (!alternateVersionsOfPrimary.Any(i => i.ItemId.HasValue && i.ItemId.Value.Equals(item.Id)))
             {
                 alternateVersionsOfPrimary.Add(new LinkedChild
diff --git a/Jellyfin.Server.Implementations/Item/BaseItemRepository.cs b/Jellyfin.Server.Implementations/Item/BaseItemRepository.cs
index 9e6b100b66..22178e57f7 100644
--- a/Jellyfin.Server.Implementations/Item/BaseItemRepository.cs
+++ b/Jellyfin.Server.Implementations/Item/BaseItemRepository.cs
@@ -3843,4 +3843,43 @@ public sealed class BaseItemRepository
 
         return result;
     }
+
+    /// <inheritdoc/>
+    public IReadOnlyList<Guid> GetManualLinkedParentIds(Guid childId)
+    {
+        using var context = _dbProvider.CreateDbContext();
+        return context.LinkedChildren
+            .Where(lc => lc.ChildId == childId && lc.ChildType == DbLinkedChildType.Manual)
+            .Select(lc => lc.ParentId)
+            .Distinct()
+            .ToList();
+    }
+
+    /// <inheritdoc/>
+    public int RerouteLinkedChildren(Guid fromChildId, Guid toChildId)
+    {
+        using var context = _dbProvider.CreateDbContext();
+
+        // Get parents that already reference toChildId (to avoid duplicates)
+        var parentsWithTarget = context.LinkedChildren
+            .Where(lc => lc.ChildId == toChildId && lc.ChildType == DbLinkedChildType.Manual)
+            .Select(lc => lc.ParentId)
+            .ToHashSet();
+
+        // Update references that won't create duplicates
+        var updated = context.LinkedChildren
+            .Where(lc => lc.ChildId == fromChildId
+                && lc.ChildType == DbLinkedChildType.Manual
+                && !parentsWithTarget.Contains(lc.ParentId))
+            .ExecuteUpdate(s => s.SetProperty(e => e.ChildId, toChildId));
+
+        // Remove references that would be duplicates
+        context.LinkedChildren
+            .Where(lc => lc.ChildId == fromChildId
+                && lc.ChildType == DbLinkedChildType.Manual
+                && parentsWithTarget.Contains(lc.ParentId))
+            .ExecuteDelete();
+
+        return updated;
+    }
 }
diff --git a/MediaBrowser.Controller/Library/ILibraryManager.cs b/MediaBrowser.Controller/Library/ILibraryManager.cs
index c19d15d85f..48859de04b 100644
--- a/MediaBrowser.Controller/Library/ILibraryManager.cs
+++ b/MediaBrowser.Controller/Library/ILibraryManager.cs
@@ -714,5 +714,14 @@ namespace MediaBrowser.Controller.Library
         /// <param name="virtualFolderPath">The path to the virtualfolder.</param>
         /// <param name="pathInfo">The new virtualfolder.</param>
         public void CreateShortcut(string virtualFolderPath, MediaPathInfo pathInfo);
+
+        /// <summary>
+        /// Re-routes LinkedChildren references from one child to another.
+        /// Used when video versions change to maintain playlist/BoxSet integrity.
+        /// </summary>
+        /// <param name="fromChildId">The child ID to re-route from.</param>
+        /// <param name="toChildId">The child ID to re-route to.</param>
+        /// <returns>Number of references updated.</returns>
+        int RerouteLinkedChildReferences(Guid fromChildId, Guid toChildId);
     }
 }
diff --git a/MediaBrowser.Controller/Persistence/IItemRepository.cs b/MediaBrowser.Controller/Persistence/IItemRepository.cs
index f7ed39730e..504adff86c 100644
--- a/MediaBrowser.Controller/Persistence/IItemRepository.cs
+++ b/MediaBrowser.Controller/Persistence/IItemRepository.cs
@@ -210,4 +210,21 @@ public interface IItemRepository
     /// <param name="userId">The user ID for access filtering.</param>
     /// <returns>Dictionary mapping parent ID to child count.</returns>
     Dictionary<Guid, int> GetChildCountBatch(IReadOnlyList<Guid> parentIds, Guid? userId);
+
+    /// <summary>
+    /// Gets parent IDs (Playlists/BoxSets) that reference the specified child with LinkedChildType.Manual.
+    /// </summary>
+    /// <param name="childId">The child item ID.</param>
+    /// <returns>List of parent IDs that reference the child.</returns>
+    IReadOnlyList<Guid> GetManualLinkedParentIds(Guid childId);
+
+    /// <summary>
+    /// Updates LinkedChildren references from one child to another, preserving SortOrder.
+    /// Handles duplicates: if parent already references toChildId, removes the old reference instead.
+    /// Used when video versions change to maintain collection integrity.
+    /// </summary>
+    /// <param name="fromChildId">The child ID to re-route from.</param>
+    /// <param name="toChildId">The child ID to re-route to.</param>
+    /// <returns>Number of references updated.</returns>
+    int RerouteLinkedChildren(Guid fromChildId, Guid toChildId);
 }