I had the same issue in converting to 4.12. To fix it I did the following:
Launched the 4.11 project and disabled the non-built in plug in.
Opened the 4.11 project in Visual Studio 2015 and did a Clean Solution.
Closed Unreal Editor Project and Visual Studio project.
Launched the 4.12.3 Unreal Engine and then the Convert / Copy To worked flawlessly.