diff -ur portage-2.1.2.orig/pym/portage.py portage-2.1.2/pym/portage.py
--- portage-2.1.2.orig/pym/portage.py	2007-02-01 21:33:13.000000000 -0500
+++ portage-2.1.2/pym/portage.py	2007-02-01 21:34:32.000000000 -0500
@@ -6788,7 +6788,7 @@
 		return pkgfiles
 
 	def unmerge(self, pkgfiles=None, trimworld=1, cleanup=1,
-		ldpath_mtimes=None):
+		ldpath_mtimes=None, alreadyinstalled=0):
 		"""
 		Calls prerm
 		Unmerges a given package (CPV)
@@ -6867,7 +6867,7 @@
 					writemsg("!!! FAILED prerm: %s\n" % retval, noiselevel=-1)
 					return retval
 
-			self._unmerge_pkgfiles(pkgfiles)
+			self._unmerge_pkgfiles(pkgfiles, alreadyinstalled=alreadyinstalled)
 
 			if myebuildpath:
 				retval = doebuild(myebuildpath, "postrm", self.myroot,
@@ -6906,7 +6906,7 @@
 			contents=contents)
 		return os.EX_OK
 
-	def _unmerge_pkgfiles(self, pkgfiles):
+	def _unmerge_pkgfiles(self, pkgfiles, alreadyinstalled=0):
 		"""
 		
 		Unmerges the contents of a package from the liveFS
@@ -7014,11 +7014,38 @@
 			mydirs.sort()
 			mydirs.reverse()
 
+			# Get a list of versions for this package to check empty directories
+			otherversions=[]
+			for v in self.vartree.dbapi.cp_list(self.mysplit[0]):
+				otherversions.append(v.split("/")[1])
+			# Remove ourselves only if we're upgrading
+			# If alreadyinstalled is set, we're only replacing ourself with the same package
+			if not alreadyinstalled and self.pkg in otherversions:
+				otherversions.remove(self.pkg)
+
+			otherpkglist = []
+			destroot = '/' # Setup this for convenience since we only unmerge live packages
+			for v in otherversions:
+				# Actual dblink object since package names are not useful
+				otherpkglist.append(
+					dblink(self.cat, v, destroot, self.settings, vartree = self.vartree))
+				
 			for obj in mydirs:
-				try:
-					os.rmdir(obj)
-					writemsg_stdout("<<<        %s %s\n" % ("dir",obj))
-				except (OSError, IOError):
+				# The directory is empty, then check before removing
+				if len(os.listdir(obj)) == 0:
+					for p in otherpkglist:
+						if p.isowner(obj, destroot):
+							break
+					else:
+						# Nothing else owns the directory
+						os.rmdir(obj)
+						writemsg_stdout("<<<        %s %s\n" % ("dir",obj))
+						continue
+					
+					# Execution reaches here if something owns the directory
+					writemsg_stdout("--- !keep dir %s\n" % obj)
+				else:
+					# This is for directories that are not empty
 					writemsg_stdout("--- !empty dir %s\n" % obj)
 
 		#remove self from vartree database so that our own virtual gets zapped if we're the last node
@@ -7353,7 +7380,7 @@
 		if os.path.exists(self.dbpkgdir):
 			writemsg_stdout(">>> Safely unmerging already-installed instance...\n")
 			self.dbdir = self.dbpkgdir
-			self.unmerge(oldcontents, trimworld=0, ldpath_mtimes=prev_mtimes)
+			self.unmerge(oldcontents, trimworld=0, ldpath_mtimes=prev_mtimes, alreadyinstalled=1)
 			self.dbdir = self.dbtmpdir
 			writemsg_stdout(">>> Original instance of package unmerged safely.\n")