diff --git a/File_Format_Library/FileFormats/Layout/CAFE/Header.cs b/File_Format_Library/FileFormats/Layout/CAFE/Header.cs
index b5c3ee5d..2597e476 100644
--- a/File_Format_Library/FileFormats/Layout/CAFE/Header.cs
+++ b/File_Format_Library/FileFormats/Layout/CAFE/Header.cs
@@ -450,8 +450,16 @@ namespace LayoutBXLYT.Cafe
 
         public void Write(FileWriter writer)
         {
+            RecalculateMaterialReferences();
+
             Version = VersionMajor << 24 | VersionMinor << 16 | VersionMicro << 8 | VersionMicro2;
 
+            foreach (var pane in PaneLookup.Values)
+            {
+                if (pane is PIC1)
+                    ((PIC1)pane).MaterialIndex = (ushort)MaterialList.Materials.IndexOf(((PIC1)pane).Material);
+            }
+
             writer.SetByteOrder(true);
             writer.WriteSignature(Magic);
             if (!IsBigEndian)
diff --git a/File_Format_Library/FileFormats/Layout/CTR/BCLYT.cs b/File_Format_Library/FileFormats/Layout/CTR/BCLYT.cs
index c8982567..fa7dd9cc 100644
--- a/File_Format_Library/FileFormats/Layout/CTR/BCLYT.cs
+++ b/File_Format_Library/FileFormats/Layout/CTR/BCLYT.cs
@@ -479,6 +479,8 @@ namespace LayoutBXLYT
 
             public void Write(FileWriter writer)
             {
+                RecalculateMaterialReferences();
+
                 Version = VersionMajor << 24 | VersionMinor << 16 | VersionMicro << 8 | VersionMicro2;
 
                 writer.SetByteOrder(true);
diff --git a/File_Format_Library/FileFormats/Layout/Common.cs b/File_Format_Library/FileFormats/Layout/Common.cs
index 6e5917e8..0045066e 100644
--- a/File_Format_Library/FileFormats/Layout/Common.cs
+++ b/File_Format_Library/FileFormats/Layout/Common.cs
@@ -2285,6 +2285,24 @@ namespace LayoutBXLYT
             return new BxlytMaterial();
         }
 
+        public void RecalculateMaterialReferences()
+        {
+            List<BxlytMaterial> materials = Materials;
+            foreach (var pane in PaneLookup.Values)
+            {
+                if (pane is IPicturePane)
+                    ((IPicturePane)pane).MaterialIndex = (ushort)materials.IndexOf(((IPicturePane)pane).Material);
+                if (pane is IWindowPane)
+                {
+                    ((IWindowPane)pane).Content.MaterialIndex = (ushort)materials.IndexOf(((IWindowPane)pane).Content.Material);
+                    foreach (var window in ((IWindowPane)pane).WindowFrames)
+                        window.MaterialIndex = (ushort)materials.IndexOf(window.Material);
+                }
+                if (pane is ITextPane)
+                    ((ITextPane)pane).MaterialIndex = (ushort)materials.IndexOf(((ITextPane)pane).Material);
+            }
+        }
+
         public void RemoveTextureReferences(string texture)
         {
             foreach (var mat in Materials)