By default portage saves all files that are in CONFIG_PROTECT path, these feature is very usefull but it leads to many unneeded files in /etc directory (mostly from packages that You just wanned to test or old ebuilds that were not needed any more and were unmerged). Solution to problem could be adding new command line option to the portage that would make portage ask user what to do with every file that is in CONFIG_PROTECT, he could save the file, delete it or mayby move the file to other location.
*** This bug has been marked as a duplicate of 8423 ***