diff --git a/package/base-files/files/sbin/sysupgrade b/package/base-files/files/sbin/sysupgrade
index ef83c4b00f..93f0749108 100755
--- a/package/base-files/files/sbin/sysupgrade
+++ b/package/base-files/files/sbin/sysupgrade
@@ -115,6 +115,7 @@ add_overlayfiles() {
 		local overlaydir="/overlay"
 	fi
 	find $overlaydir/etc/ -type f -o -type l | sed \
+		-e 's,^/overlay\/upper/,/,' \
 		-e 's,^/overlay/,/,' \
 		-e '\,/META_[a-zA-Z0-9]*$,d' \
 		-e '\,/functions.sh$,d' \