I've installed a package which was already installed and listed in my world file by using ebuild instead of emerge (I had to patch the source). To my surprise, the ebuild install silently *removed* the package from my world file. Hence, it was no longer auto-updated. Why?
I know, this is so incredibly annoying! I often install other versions than what portage recommends, and when I do that they get removed from the world file. What's the point of removing programs emerged via ebuilds?
Have you verified this in a 2.0.47 series portage? What version are you using currently?
Made a single test with portage 47-r8, and the problem did *not* happen. No idea if I just had good luck or did something different from what I did originally, or if the problem has really been solved.
I'm betting it was related to the general world-depleting bug I fixed for the 47 series.