Index: usr.sbin/freebsd-update/freebsd-update.sh
===================================================================
--- usr.sbin/freebsd-update/freebsd-update.sh
+++ usr.sbin/freebsd-update/freebsd-update.sh
@@ -2906,8 +2906,21 @@
 	sort -k 1,1 -t '|' $1 |
 	    tr '|' ' ' |
 	    while read FPATH TYPE OWNER GROUP PERM FLAGS HASH LINK; do
+		if [ -e ${BASEDIR}/${FPATH} ]; then
+			if [ ${TYPE} = d ] && ! [ -d ${BASEDIR}/${FPATH} ]; then
+				rm -f ${BASEDIR}/${FPATH}
+			elif [ ${TYPE} = 'f' || ${TYPE} = 'L' ] && \
+			    [ -d ${BASEDIR}/${FPATH} ]; then
+				rm -rf ${BASEDIR}/${FPATH}
+			fi
+		fi
 		case ${TYPE} in
 		d)
+	        	if [ -e ${BASEDIR}/${FPATH} ] && \
+			    ! [ -d ${BASEDIR}/${FPATH} ]; then
+				# Exists but not a directory
+				rm -f ${BASEDIR}/${FPATH}
+			fi
 			# Create a directory
 			install -d -o ${OWNER} -g ${GROUP}		\
 			    -m ${PERM} ${BASEDIR}/${FPATH}