Core: Save the disabling of default enabled codes

The previous commit adjusted the code for loading
and this commit adjusts the code for saving.

Source/Core/Core/PatchEngine.h

@@ -34,6 +34,7 @@ struct Patch
   std::string name;
   std::vector<PatchEntry> entries;
   bool enabled = false;
+  bool default_enabled = false;
   bool user_defined = false;  // False if this code is shipped with Dolphin.
 };