I built 4.2.0.0 and was able to build the Editor fine. However, opening up ShooterDemo 4.1 and trying to convert to 4.2 would not build and I got the same exact error.
1>------ Build started: Project: UE4, Configuration: Debug_Game Win32 ------
1>EXEC : error : Couldn't find referenced module 'SubstanceCore'.
1>H:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.MakeFile.Targets(38,5): error MSB3073: The command "C:\UnrealEngine\UnrealEngineSubstancePlugin\UnrealEngine\Engine\Build\BatchFiles\Build.bat UE4Game Win32 Debug" exited with code -1.
========== Build: 0 succeeded, 1 failed, 1 up-to-date, 0 skipped ==========