Visual Studio Addin creates bad project file if "flat" flag is removed from config before converting to Visual Studio project

When removing the "flat" flag (CONFIG -= flat), opening a qt pro file generates bad Visual Studio project file.

Following warning is shown to user:
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppBuild.targets(942,5): warning MSB8027: Two or more files with the name of qrc_qml.cpp will produce outputs to the same location. This can lead to an incorrect build result. The files involved are GeneratedFiles\qrc_qml.cpp, debug\qrc_qml.cpp.

And the build stops to a following error:
c1xx : fatal error C1083: Cannot open source file: 'debug\qrc_qml.cpp': No such file or directory

Steps to reproduce:

• Create empty Qt Quick Application project
• Add "CONFIG -= flat" to the project file
• Open the project file through Visual Studio Addin -> Open Qt Project file
• Start building
• EXPECTED: Build succeeds without warnings
• ACTUAL: Previous warning is shown, and build does not complete because of the previous error message

Observing the Solution Explorer shows that the qml_qrc.cpp file is included twice in the project. Attached a screenshot of this situation.