Thats indeed only for vs.net 2005. When you generate, llblgen pro's project file task performer (which creates the project file) adds an xml element to the file element in the project file to signal that the file is generated. When you set clean vs.net projects to true, the files with that element are removed first, and then the ones generated are added again.
Do you experience a different situation? Are your partial classes removed? Because that's not what it should be doing