Why IgnoreFileChanges doesn't work in Project files?

I need to save the project file programatically after some add/remove file operation. However no matter how I do the "Project File has changed and must be reloaded" message pops up always.

Im coding through Managed Package Framework, but seeing how it calls the 

IVsDocDataFileChangeControl.IgnoreFileChanges and 

IVsFileChangeEx.IgnoreFile

in the SuspendFileChanges.cs file, the calls seems correct. No errors are generated.

Btw I am saving through Project Automation API. If I execute the "SaveAll" command through DTE it works fine, but then it saves ALL documents too, not only the project.