during the emerge update process, several versions of a package can be installed. after that, trying to unmerge the old version will remove empty directories common to both the old and the new package, thus possibly damaging the installation of the new package.
make a .keep in the ebuilds. Empty directories are assumed unneeded which is a practical solution. An ebuild should have .keep's for a directory that needs to be persistant. This will maintain the directory and it's ownership to the newest package.
