fix node duplication in update after external changes.

doc/classes/Node.xml

@@ -795,8 +795,9 @@
 			<return type="void" />
 			<param index="0" name="node" type="Node" />
 			<param index="1" name="keep_groups" type="bool" default="false" />
+			<param index="2" name="keep_children" type="bool" default="true" />
 			<description>
-				Replaces this node by the given [param node]. All children of this node are moved to [param node].
+				Replaces this node by the given [param node]. If [param keep_children] is [code]true[/code] all children of this node are moved to [param node].
 				If [param keep_groups] is [code]true[/code], the [param node] is added to the same groups that the replaced node is in (see [method add_to_group]).
 				[b]Warning:[/b] The replaced node is removed from the tree, but it is [b]not[/b] deleted. To prevent memory leaks, store a reference to the node in a variable, or use [method Object.free].
 			</description>

editor/editor_data.cpp

@@ -722,15 +722,8 @@ bool EditorData::check_and_update_scene(int p_idx) {
 
 		new_scene->set_scene_file_path(edited_scene[p_idx].root->get_scene_file_path());
 		Node *old_root = edited_scene[p_idx].root;
-		for (int i = 0; i < old_root->get_child_count(); i++) {
-			memdelete(old_root->get_child(i));
-		}
-		old_root->replace_by(new_scene);
+		old_root->replace_by(new_scene, false, false);
 		memdelete(old_root);
-		edited_scene.write[p_idx].root = new_scene;
-		if (!new_scene->get_scene_file_path().is_empty()) {
-			edited_scene.write[p_idx].path = new_scene->get_scene_file_path();
-		}
 		edited_scene.write[p_idx].selection = new_selection;
 
 		return true;

editor/editor_node.cpp

@@ -3818,6 +3818,14 @@ void EditorNode::_set_current_scene_nocheck(int p_idx) {
 		}
 	}
 
+	if (editor_data.check_and_update_scene(p_idx)) {
+		if (!editor_data.get_scene_path(p_idx).is_empty()) {
+			editor_folding.load_scene_folding(editor_data.get_edited_scene_root(p_idx), editor_data.get_scene_path(p_idx));
+		}
+
+		EditorUndoRedoManager::get_singleton()->clear_history(false, editor_data.get_scene_history_id(p_idx));
+	}
+
 	Dictionary state = editor_data.restore_edited_scene_state(editor_selection, &editor_history);
 	_edit_current(true);
 
@@ -3827,14 +3835,6 @@ void EditorNode::_set_current_scene_nocheck(int p_idx) {
 	if (tabs_to_close.is_empty()) {
 		callable_mp(this, &EditorNode::_set_main_scene_state).call_deferred(state, get_edited_scene()); // Do after everything else is done setting up.
 	}
-
-	if (editor_data.check_and_update_scene(p_idx)) {
-		if (!editor_data.get_scene_path(p_idx).is_empty()) {
-			editor_folding.load_scene_folding(editor_data.get_edited_scene_root(p_idx), editor_data.get_scene_path(p_idx));
-		}
-
-		EditorUndoRedoManager::get_singleton()->clear_history(false, editor_data.get_scene_history_id(p_idx));
-	}
 }
 
 void EditorNode::setup_color_picker(ColorPicker *p_picker) {

misc/extension_api_validation/4.2-stable.expected

@@ -248,3 +248,10 @@ Validate extension JSON: Error: Field 'classes/AcceptDialog/methods/register_tex
 Validate extension JSON: Error: Field 'classes/AcceptDialog/methods/remove_button/arguments/0': type changed value in new API, from "Control" to "Button".
 
 Changed argument type to the more specific one actually expected by the method. Compatibility method registered.
+
+
+GH-89992
+--------
+Validate extension JSON: Error: Field 'classes/Node/methods/replace_by/arguments': size changed value in new API, from 2 to 3.
+
+Added optional argument to prevent children to be reparented during replace_by. Compatibility method registered.

scene/main/node.compat.inc

@@ -0,0 +1,41 @@
+/**************************************************************************/
+/*  node.compat.inc                                                       */
+/**************************************************************************/
+/*                         This file is part of:                          */
+/*                             GODOT ENGINE                               */
+/*                        https://godotengine.org                         */
+/**************************************************************************/
+/* Copyright (c) 2014-present Godot Engine contributors (see AUTHORS.md). */
+/* Copyright (c) 2007-2014 Juan Linietsky, Ariel Manzur.                  */
+/*                                                                        */
+/* Permission is hereby granted, free of charge, to any person obtaining  */
+/* a copy of this software and associated documentation files (the        */
+/* "Software"), to deal in the Software without restriction, including    */
+/* without limitation the rights to use, copy, modify, merge, publish,    */
+/* distribute, sublicense, and/or sell copies of the Software, and to     */
+/* permit persons to whom the Software is furnished to do so, subject to  */
+/* the following conditions:                                              */
+/*                                                                        */
+/* The above copyright notice and this permission notice shall be         */
+/* included in all copies or substantial portions of the Software.        */
+/*                                                                        */
+/* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,        */
+/* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF     */
+/* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. */
+/* IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY   */
+/* CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,   */
+/* TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE      */
+/* SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                 */
+/**************************************************************************/
+
+#ifndef DISABLE_DEPRECATED
+
+void Node::_replace_by_bind_compat_89992(Node *p_node, bool p_keep_data) {
+	replace_by(p_node, p_keep_data, true);
+}
+
+void Node::_bind_compatibility_methods() {
+	ClassDB::bind_compatibility_method(D_METHOD("replace_by", "node", "keep_groups"), &Node::_replace_by_bind_compat_89992, DEFVAL(false));
+}
+
+#endif

scene/main/node.cpp

@@ -29,6 +29,7 @@
 /**************************************************************************/
 
 #include "node.h"
+#include "node.compat.inc"
 
 #include "core/config/project_settings.h"
 #include "core/core_string_names.h"
@@ -3007,7 +3008,7 @@ static void find_owned_by(Node *p_by, Node *p_node, List<Node *> *p_owned) {
 	}
 }
 
-void Node::replace_by(Node *p_node, bool p_keep_groups) {
+void Node::replace_by(Node *p_node, bool p_keep_groups, bool p_keep_children) {
 	ERR_THREAD_GUARD
 	ERR_FAIL_NULL(p_node);
 	ERR_FAIL_COND(p_node->data.parent);
@@ -3028,13 +3029,13 @@ void Node::replace_by(Node *p_node, bool p_keep_groups) {
 	_replace_connections_target(p_node);
 
 	if (data.owner) {
-		for (int i = 0; i < get_child_count(); i++) {
-			find_owned_by(data.owner, get_child(i), &owned_by_owner);
+		if (p_keep_children) {
+			for (int i = 0; i < get_child_count(); i++) {
+				find_owned_by(data.owner, get_child(i), &owned_by_owner);
+			}
 		}
-
 		_clean_up_owner();
 	}
-
 	Node *parent = data.parent;
 	int index_in_parent = get_index(false);
 
@@ -3046,31 +3047,33 @@ void Node::replace_by(Node *p_node, bool p_keep_groups) {
 
 	emit_signal(SNAME("replacing_by"), p_node);
 
-	while (get_child_count()) {
-		Node *child = get_child(0);
-		remove_child(child);
-		if (!child->is_owned_by_parent()) {
-			// add the custom children to the p_node
-			Node *child_owner = child->get_owner() == this ? p_node : child->get_owner();
-			child->set_owner(nullptr);
-			p_node->add_child(child);
-			child->set_owner(child_owner);
+	if (p_keep_children) {
+		while (get_child_count()) {
+			Node *child = get_child(0);
+			remove_child(child);
+			if (!child->is_owned_by_parent()) {
+				// add the custom children to the p_node
+				Node *child_owner = child->get_owner() == this ? p_node : child->get_owner();
+				child->set_owner(nullptr);
+				p_node->add_child(child);
+				child->set_owner(child_owner);
+			}
 		}
-	}
 
-	p_node->set_owner(owner);
-	for (Node *E : owned) {
-		if (E->data.owner != p_node) {
-			E->set_owner(p_node);
+		for (Node *E : owned) {
+			if (E->data.owner != p_node) {
+				E->set_owner(p_node);
+			}
 		}
-	}
 
-	for (Node *E : owned_by_owner) {
-		if (E->data.owner != owner) {
-			E->set_owner(owner);
+		for (Node *E : owned_by_owner) {
+			if (E->data.owner != owner) {
+				E->set_owner(owner);
+			}
 		}
 	}
 
+	p_node->set_owner(owner);
 	p_node->set_scene_file_path(get_scene_file_path());
 }
 
@@ -3597,7 +3600,7 @@ void Node::_bind_methods() {
 	ClassDB::bind_method(D_METHOD("create_tween"), &Node::create_tween);
 
 	ClassDB::bind_method(D_METHOD("duplicate", "flags"), &Node::duplicate, DEFVAL(DUPLICATE_USE_INSTANTIATION | DUPLICATE_SIGNALS | DUPLICATE_GROUPS | DUPLICATE_SCRIPTS));
-	ClassDB::bind_method(D_METHOD("replace_by", "node", "keep_groups"), &Node::replace_by, DEFVAL(false));
+	ClassDB::bind_method(D_METHOD("replace_by", "node", "keep_groups", "keep_children"), &Node::replace_by, DEFVAL(false), DEFVAL(true));
 
 	ClassDB::bind_method(D_METHOD("set_scene_instance_load_placeholder", "load_placeholder"), &Node::set_scene_instance_load_placeholder);
 	ClassDB::bind_method(D_METHOD("get_scene_instance_load_placeholder"), &Node::get_scene_instance_load_placeholder);

scene/main/node.h

@@ -310,6 +310,11 @@ class Node : public Object {
 	Variant _call_thread_safe_bind(const Variant **p_args, int p_argcount, Callable::CallError &r_error);
 
 protected:
+#ifndef DISABLE_DEPRECATED
+	void _replace_by_bind_compat_89992(Node *p_node, bool p_keep_data = false);
+	static void _bind_compatibility_methods();
+#endif // DISABLE_DEPRECATED
+
 	void _block() { data.blocked++; }
 	void _unblock() { data.blocked--; }
 
@@ -629,7 +634,7 @@ class Node : public Object {
 		return binds;
 	}
 
-	void replace_by(Node *p_node, bool p_keep_data = false);
+	void replace_by(Node *p_node, bool p_keep_groups = false, bool p_keep_children = true);
 
 	void set_process_mode(ProcessMode p_mode);
 	ProcessMode get_process_mode() const;