I wasn't able to fix the locking of the files, but I reordered the scanner to first perform the metadata download then try and generate cover images.

API/Program.cs

@@ -20,9 +20,11 @@ using Microsoft.Extensions.Configuration;
 using Microsoft.Extensions.DependencyInjection;
 using Microsoft.Extensions.Hosting;
 using Microsoft.Extensions.Logging;
+using NetVips;
 using Serilog;
 using Serilog.Events;
 using Serilog.Sinks.AspNetCore.SignalR.Extensions;
+using Log = Serilog.Log;
 
 namespace API;
 #nullable enable
@@ -143,6 +145,8 @@ public class Program
             var settings = await unitOfWork.SettingsRepository.GetSettingsDtoAsync();
             LogLevelOptions.SwitchLogLevel(settings.LoggingLevel);
 
+            InitNetVips();
+
             await host.RunAsync();
         } catch (Exception ex)
         {
@@ -225,4 +229,14 @@ public class Program
 
                 webBuilder.UseStartup<Startup>();
             });
+
+    /// <summary>
+    /// Ensure NetVips does not cache
+    /// </summary>
+    /// <remarks>https://github.com/kleisauke/net-vips/issues/6#issuecomment-394379299</remarks>
+    private static void InitNetVips()
+    {
+        Cache.MaxFiles = 0;
+
+    }
 }

API/Services/DirectoryService.cs

@@ -1112,4 +1112,23 @@ public class DirectoryService : IDirectoryService
             FlattenDirectory(root, subDirectory, ref directoryIndex);
         }
     }
+
+    /// <summary>
+    /// If the file is locked or not existing
+    /// </summary>
+    /// <param name="filePath"></param>
+    /// <returns></returns>
+    public static bool IsFileLocked(string filePath)
+    {
+        try
+        {
+            if (!File.Exists(filePath)) return false;
+            using var stream = new FileStream(filePath, FileMode.Open, FileAccess.Read, FileShare.None);
+            return false; // If this works, the file is not locked
+        }
+        catch (IOException)
+        {
+            return true; // File is locked by another process
+        }
+    }
 }

API/Services/Tasks/Metadata/CoverDbService.cs

@@ -643,10 +643,8 @@ public class CoverDbService : ICoverDbService
 
                         if (choseNewImage)
                         {
-
-                            File.Delete(existingPath);
-
-                            //_directoryService.DeleteFiles([existingPath]);
+                            // This will fail if Cover gen is done just before this as there is a bug with files getting locked.
+                            _directoryService.DeleteFiles([existingPath]);
                             _directoryService.CopyFile(tempFullPath, finalFullPath);
                             _directoryService.DeleteFiles([tempFullPath]);
                         }
@@ -698,11 +696,11 @@ public class CoverDbService : ICoverDbService
     ///
     /// </summary>
     /// <param name="url"></param>
-    /// <param name="filename"></param>
+    /// <param name="filenameWithoutExtension">Filename without extension</param>
     /// <param name="fromBase64"></param>
     /// <param name="targetDirectory">Not useable with fromBase64. Allows a different directory to be written to</param>
     /// <returns></returns>
-    private async Task<string> CreateThumbnail(string url, string filename, bool fromBase64 = true, string? targetDirectory = null)
+    private async Task<string> CreateThumbnail(string url, string filenameWithoutExtension, bool fromBase64 = true, string? targetDirectory = null)
     {
         targetDirectory ??= _directoryService.CoverImageDirectory;
 
@@ -713,9 +711,9 @@ public class CoverDbService : ICoverDbService
         if (fromBase64)
         {
             return _imageService.CreateThumbnailFromBase64(url,
-                filename, encodeFormat, coverImageSize.GetDimensions().Width);
+                filenameWithoutExtension, encodeFormat, coverImageSize.GetDimensions().Width);
         }
 
-        return await DownloadImageFromUrl(filename, encodeFormat, url, targetDirectory);
+        return await DownloadImageFromUrl(filenameWithoutExtension, encodeFormat, url, targetDirectory);
     }
 }

API/Services/Tasks/Scanner/ProcessSeries.cs

@@ -194,8 +194,8 @@ public class ProcessSeries : IProcessSeries
                 if (seriesAdded)
                 {
                     // See if any recommendations can link up to the series and pre-fetch external metadata for the series
-                    BackgroundJob.Enqueue(() =>
-                        _externalMetadataService.FetchSeriesMetadata(series.Id, series.Library.Type));
+                    // BackgroundJob.Enqueue(() =>
+                    //     _externalMetadataService.FetchSeriesMetadata(series.Id, series.Library.Type));
 
                     await _eventHub.SendMessageAsync(MessageFactory.SeriesAdded,
                         MessageFactory.SeriesAddedEvent(series.Id, series.Name, series.LibraryId), false);
@@ -214,6 +214,10 @@ public class ProcessSeries : IProcessSeries
             return;
         }
 
+        if (seriesAdded)
+        {
+            await _externalMetadataService.FetchSeriesMetadata(series.Id, series.Library.Type);
+        }
         await _metadataService.GenerateCoversForSeries(series.LibraryId, series.Id, false, false);
         await _wordCountAnalyzerService.ScanSeries(series.LibraryId, series.Id, forceUpdate);
     }