.cobolbuild not getting updated in Visual Cobol 6.0 Eclipse

Hi there

Usually I build my Project using "Project -> Build Project" in VC Eclipse IDE. I do have different SQL Pre-processor settings which are at file and folder level.

Recently I wanted to try the ant build and when I checked the .cobolBuild file it doesn't seem to match my Project build settings. Particularly, the sql pre-processor settings are not updated in .cobolbuild file. 

Is this a manual activity? It is very difficult to update the .cobolbuild file with more than 3000+ source files.