Users are not expected to be able to manipulate the project in this way. The overwriting of the include paths during project regeneration is not a supported workflow, so this will not be fixed.
Adding a new code class to a code project, or generating code files, will reset any Include Directories set in the Project Properties in Visual Studio.
Include Directories is blank again.
Include Directories still contains the settings previously specified.
Head over to the existing Questions & Answers thread and let us know what's up.