diff --git a/setup_board b/setup_board
index ad1816cf65..70080ce1bd 100755
--- a/setup_board
+++ b/setup_board
@@ -240,8 +240,9 @@ if [ "${FLAGS_skip_toolchain_update}" -eq "${FLAGS_TRUE}" ]; then
   UPDATE_ARGS+=" --skip_toolchain_update"
 fi
 if [ "${FLAGS_skip_chroot_upgrade}" -eq "${FLAGS_FALSE}" ] ; then
-  "${SRC_ROOT}/scripts"/update_chroot ${UPDATE_ARGS}
+	:
 fi
+"${SRC_ROOT}/scripts"/update_chroot ${UPDATE_ARGS}
 
 # Migrate board roots that were created before the package location
 # was standardized to /var/lib/portage/pkgs, build_image will fail if we
diff --git a/update_chroot b/update_chroot
index cbd58caa5a..a322319557 100755
--- a/update_chroot
+++ b/update_chroot
@@ -103,15 +103,13 @@ EMERGE_DEFAULT_OPTS="--verbose --oneshot"
 source "/etc/portage/make.conf.user"
 EOF
 
-sudo_clobber "/etc/portage/repos.conf/gentoo-subset.conf" <<EOF
+sudo_clobber "/etc/portage/repos.conf/coreos.conf" <<EOF
 [DEFAULT]
 main-repo = gentoo-subset
 
 [gentoo-subset]
 location = ${GENTOO_SUBSET_OVERLAY}
-EOF
 
-sudo_clobber "/etc/portage/repos.conf/flatcar-overlay.conf" <<EOF
 [flatcar-overlay]
 location = ${FLATCAR_OVERLAY}
 EOF