diff --git a/RecodeItGUI/GUI/Main.cs b/RecodeItGUI/GUI/Main.cs
index 43f5ee9..044205a 100644
--- a/RecodeItGUI/GUI/Main.cs
+++ b/RecodeItGUI/GUI/Main.cs
@@ -275,6 +275,8 @@ public partial class ReCodeItForm : Form
 
         DataProvider.LoadMappingFile(result);
         AppSettings.Remapper.MappingPath = result;
+        AppSettings.Remapper.UseProjectMappings = false;
+        ActiveProjectMappingsCheckbox.Checked = false;
         DataProvider.SaveAppSettings();
 
         LoadedMappingFilePath.Text = result;
diff --git a/RecodeItLib/CrossCompiler/ReCodeItCrossCompiler.cs b/RecodeItLib/CrossCompiler/ReCodeItCrossCompiler.cs
index d031944..25eb14f 100644
--- a/RecodeItLib/CrossCompiler/ReCodeItCrossCompiler.cs
+++ b/RecodeItLib/CrossCompiler/ReCodeItCrossCompiler.cs
@@ -24,7 +24,12 @@ public class ReCodeItCrossCompiler
     public void StartRemap()
     {
         ChangedTypes.Clear();
-        Remapper.InitializeRemap(ActiveProject.OriginalAssemblyPath, ActiveProject.RemappedAssemblyPath, true);
+
+        Remapper.InitializeRemap(
+            ActiveProject.RemapModels,
+            ActiveProject.OriginalAssemblyPath,
+            ActiveProject.RemappedAssemblyPath,
+            true);
 
         if (ActiveProject == null)
         {