Index: pym/portage.py
===================================================================
--- pym/portage.py	(revision 6848)
+++ pym/portage.py	(revision 6853)
@@ -7158,13 +7158,16 @@
 					writemsg_stdout("--- cfgpro %s %s\n" % (pkgfiles[objkey][0], obj))
 					continue
 
+				# Don't unlink symlinks to directories here since that can
+				# remove /lib and /usr/lib symlinks.
 				if unmerge_orphans and \
 					lstatobj and not stat.S_ISDIR(lstatobj.st_mode) and \
+					not (islink and statobj and stat.S_ISDIR(statobj.st_mode)) and \
 					not self.isprotected(obj):
 					try:
 						# Remove permissions to ensure that any hardlinks to
 						# suid/sgid files are rendered harmless.
-						if statobj:
+						if statobj and not islink:
 							os.chmod(obj, 0)
 						os.unlink(obj)
 					except EnvironmentError, e:
@@ -7186,6 +7189,11 @@
 					if not islink:
 						writemsg_stdout("--- !sym   %s %s\n" % ("sym", obj))
 						continue
+					# Don't unlink symlinks to directories here since that can
+					# remove /lib and /usr/lib symlinks.
+					if statobj and stat.S_ISDIR(statobj.st_mode):
+						writemsg_stdout("--- !sym   %s %s\n" % ("sym", obj))
+						continue
 					try:
 						os.unlink(obj)
 						writemsg_stdout("<<<        %s %s\n" % ("sym",obj))