add .qsys is good, add .qip of the Qsys is bad

When I remove .qsys and add .qip in project settings, the .qsf file is properly regenerated : it contains no reference to .qsys.

But I may find : my qsys system is not at the project root path, it is in a custom "src" subdirectory. Maybe the (minor) problem is this.

OK, that was the problem.

I saved my Qsys in my Quartus project root directory, deleted the old qsys, adapt project files settings, and everything is correct. :)

quartus 12.0sp1 + nios ii web edition

qsys from scratch (no sopc to qsys migration : that is to say tri-stated components are from qsys)