diff --git a/lib/northbound.c b/lib/northbound.c
index 2fabae22ba..12ca3e1006 100644
--- a/lib/northbound.c
+++ b/lib/northbound.c
@@ -236,7 +236,8 @@ void nb_config_replace(struct nb_config *config_dst,
 		config_dst->version = config_src->version;
 
 	/* Update dnode. */
-	yang_dnode_free(config_dst->dnode);
+	if (config_dst->dnode)
+		yang_dnode_free(config_dst->dnode);
 	if (preserve_source) {
 		config_dst->dnode = yang_dnode_dup(config_src->dnode);
 	} else {
diff --git a/lib/yang.c b/lib/yang.c
index 7daef79198..73f63b18e4 100644
--- a/lib/yang.c
+++ b/lib/yang.c
@@ -523,6 +523,8 @@ struct lyd_node *yang_dnode_dup(const struct lyd_node *dnode)
 
 void yang_dnode_free(struct lyd_node *dnode)
 {
+	while (dnode->parent)
+		dnode = dnode->parent;
 	lyd_free_withsiblings(dnode);
 }