Visual studio solution is not properly generated

I am building an unreal engine from github. Having my project MyGame placed inside UE source folder root.
If I generate solution files for engine and open UE4.sln I have all my projects loaded and in place.
But, if I use Editor->File->Open Visual Studio or generate project files from MyGame.uproject, than solution is populated with projects referencing wrong folders.

Hi ,

The only way I was able to see results similar to what you described was if I created a project in a different location (so that it had its own Visual Studio solution file), and then copied it into the Engine’s root folder. If you are working on a project that is located in the Engine’s root folder, it is intended that you work with the Engine’s solution (UE4.sln), instead of the project’s solution.

To correct this issue, go into your project’s root folder and delete the .sln, suo, and .sdf (if present) files. Then go to your Engine root folder and run GenerateProjectFiles.bat. Open the UE4.sln solution in Visual Studio and build your project (if no code changes have been made, this step may not be necessary, but it doesn’t hurt to do it). At this point, using File → Open Visual Studio from inside the Editor will open the correct solution, and right-clicking on your project’s .uproject file and selecting Generate Project Files will no longer create a project-specific solution file.

Yes, I had project in a separate folder before upgrading to UE4.9, when I decided to move project folder to UE source folder. So all prev generated solution files was here.
And your advice really helped.
Thanks, .