It happens in Qt-Creator 3.0-beta.
My project tree already complex enough. I have qbs file with the references to all libraries (libraries has dependencies on libraries), then i have qbs file with application. And some integration qbs file with the references to libraries qbs file and application file.

I will try to show problem the simpler situation.
Lets say we have such 3 qbs files.
integration file

Project {
 references: [
  "mylib.qbs",
  "app.qbs"
 ]
}

app:

Application {
 //....
 Depends {name: "mylib"}
}

and some describtion of mylib.
I build application and see some undefined references. I understand that need to add mylib2. then i change qbs file like this:

Project {
 references: [
  "mylib.qbs",
  "mylib2.qbs",
  "app.qbs"
 ]
}

app:

Application {
 //....
 Depends {name: "mylib"}
 Depends {name: "mylib2"}
}

Qt creator made "Evaluation" and i click "Build" - and see totaly same undefined references.

In previous Qt Creator it worked on the fly.
But now i need to delete bg file, and only then i really can recompile.