diff --git a/Wabbajack.Lib/CompilationSteps/IncludePatches.cs b/Wabbajack.Lib/CompilationSteps/IncludePatches.cs
index eeaddaf0..9f7fe5da 100644
--- a/Wabbajack.Lib/CompilationSteps/IncludePatches.cs
+++ b/Wabbajack.Lib/CompilationSteps/IncludePatches.cs
@@ -6,6 +6,7 @@ using Alphaleonis.Win32.Filesystem;
 using F23.StringSimilarity;
 using Newtonsoft.Json;
 using Wabbajack.Common;
+using Wabbajack.Lib.Downloaders;
 using Wabbajack.VirtualFileSystem;
 
 namespace Wabbajack.Lib.CompilationSteps
@@ -104,7 +105,7 @@ namespace Wabbajack.Lib.CompilationSteps
 
             if (patches.All(p => p.Item1))
             {
-                var (_, bytes, file) = patches.OrderBy(f => f.data!.Length).First();
+                var (_, bytes, file) = PickPatch(_mo2Compiler, patches);
                 e.FromHash = file.Hash;
                 e.ArchiveHashPath = file.MakeRelativePaths();
                 e.PatchID = await _compiler.IncludeFile(bytes!);
@@ -125,6 +126,29 @@ namespace Wabbajack.Lib.CompilationSteps
             return e;
         }
 
+        public static (bool, byte[], VirtualFile) PickPatch(MO2Compiler mo2Compiler, IEnumerable<(bool foundHash, byte[]? data, VirtualFile file)> patches)
+        {
+            var ordered = patches
+                .Select(f => (f.foundHash, f.data!, f.file))
+                .OrderBy(f => f.Item2.Length)
+                .ToArray();
+
+            var primaryChoice = ordered.FirstOrDefault(itm =>
+            {
+                var baseHash = itm.file.TopParent.Hash;
+                
+                // If this file doesn't come from a game use it
+                if (!mo2Compiler.GamesWithHashes.TryGetValue(baseHash, out var games))
+                    return true;
+
+                // Otherwise skip files that are not from the primary game
+                return games.Contains(mo2Compiler.CompilingGame.Game);
+            });
+            
+            // If we didn't find a file from an archive or the primary game, use a secondary game file.
+            return primaryChoice != default ? primaryChoice : ordered.FirstOrDefault();
+        }
+
         private AbsolutePath ModForFile(AbsolutePath file)
         {
             return file.RelativeTo(((MO2Compiler)_compiler).MO2ModsFolder).TopParent
diff --git a/Wabbajack.Lib/MO2Compiler.cs b/Wabbajack.Lib/MO2Compiler.cs
index 76ff79f2..708a2f2e 100644
--- a/Wabbajack.Lib/MO2Compiler.cs
+++ b/Wabbajack.Lib/MO2Compiler.cs
@@ -210,6 +210,7 @@ namespace Wabbajack.Lib
                     {
                         var files = await ClientAPI.GetExistingGameFiles(Queue, ag);
                         Utils.Log($"Including {files.Length} stock game files from {ag} as download sources");
+                        GameHashes[ag] = files.Select(f => f.Hash).ToHashSet();
 
                         IndexedArchives.AddRange(files.Select(f =>
                         {
@@ -228,6 +229,10 @@ namespace Wabbajack.Lib
                         Utils.Error(e, "Unable to find existing game files, skipping.");
                     }
                 }
+
+                GamesWithHashes = GameHashes.SelectMany(g => g.Value.Select(h => (g, h)))
+                    .GroupBy(gh => gh.h)
+                    .ToDictionary(gh => gh.Key, gh => gh.Select(p => p.g.Key).ToArray());
             }
 
             IndexedArchives = IndexedArchives.DistinctBy(a => a.File.AbsoluteName).ToList();
@@ -364,6 +369,9 @@ namespace Wabbajack.Lib
         }
 
 
+        public Dictionary<Game, HashSet<Hash>> GameHashes { get; set; } = new Dictionary<Game, HashSet<Hash>>();
+        public Dictionary<Hash, Game[]> GamesWithHashes { get; set; } = new Dictionary<Hash, Game[]>();
+
         public bool UseGamePaths { get; set; } = true;
 
         private async Task CleanInvalidArchivesAndFillState()
@@ -508,7 +516,7 @@ namespace Wabbajack.Lib
 
                     if (patches.All(p => p.Item1))
                     {
-                        var (_, bytes, file) = patches.OrderBy(f => f.data!.Length).First();
+                        var (_, bytes, file) = IncludePatches.PickPatch(this, patches);
                         pfa.FromFile = file;
                         pfa.FromHash = file.Hash;
                         pfa.ArchiveHashPath = file.MakeRelativePaths();