Code Projects with Substance plugin enabled fail to convert from 4.10 to 4.11

Converting a 4.10 project that includes the Substance Plugin to 4.11 will fail to compile.

Workaround:
Disabling / removing references to the plugin will allow the project to convert successfully.

1. Install Substance Plugin for 4.10 engine
2. Create a new 4.10 project (code based)
3. Navigate to Edit->Plugins to enable Substance plugin in the project (should be enabled by default)
4. Save and close the project
5. Open the 4.11 editor and open the 4.10 project (open a copy)

Result:
Project fails to open with an error message that it "Failed to initialize the engine (PreInit failed)."

Expected:
Project loads in 4.11 editor

Repro Rate:
3/3

4.11 Preview 4 - UnrealHeaderTool - Fail to initilize Engine