While upgrading KDE I got in another terminal this : # eix-test-obsolete -H brief The following installed packages are not in the database: kde-base/-MERGING-kdepimlibs ...
I am rather happy with such a message, because it shows that something is broken if e.g. portage was killed before it could remove the file. As concerns the "wrong" positive while running during emerge: You have to expect inconsistent output anyway if you run eix-test-obsolete during emerge, because the installed versions might suddenly change.