Windows 8.1 update erased custom theme, how to fix?..

So I am running a "custom" build of windows 8.1 Sweet as chocolate. I got an update the other day for Windows 8.1 not sure exactly what the update was but after in installed and I restarted my whole theme was gone. Take bar, explorer back color folder icons almost everything back to stock. I rolled back Windows but would really like to be able to update my laptop. How can I prevent everything from being deleted or what should I back up before I update? Shell files? Idk...

Also the update is Wndows 8.1 for x64 based-systems update KB2919355