When doing 'emerge --deep -u world', updated packages that are listed in the world file, are removed from it. As an example, I explicitly emerged reiserfstools, and made sure it was listed in the world file. Then, I synced/updated (emerge sync; emerge --deep -u world), and a new version of reiserfstools was installed. Upon looking in the world file, I noticed that reiserfstools had disappeared. I am using Portage 2.0.47-r10 (default-x86-1.4, gcc-3.2.2, glibc-2.3.2-r1).
Fixed for >=2.0.48_pre3
*** Bug 39363 has been marked as a duplicate of this bug. ***