diff --git a/editor/editor_node.cpp b/editor/editor_node.cpp
index 795a2af1ea9f..b36f74db9c46 100644
--- a/editor/editor_node.cpp
+++ b/editor/editor_node.cpp
@@ -151,6 +151,51 @@ EditorNode *EditorNode::singleton = nullptr;
 // The metadata key used to store and retrieve the version text to copy to the clipboard.
 static const String META_TEXT_TO_COPY = "text_to_copy";
 
+class AcceptDialogAutoReparent : public AcceptDialog {
+	GDCLASS(AcceptDialogAutoReparent, AcceptDialog);
+
+protected:
+	void _notification(int p_what) {
+		if (p_what == NOTIFICATION_VISIBILITY_CHANGED) {
+			if (!is_visible()) {
+				Node *p = get_parent();
+				if (p) {
+					p->remove_child(this);
+				}
+			}
+		}
+	}
+
+public:
+	void attach_and_popup_centered() {
+		EditorNode *ed = EditorNode::get_singleton();
+		if (ed && !is_inside_tree()) {
+			Window *w = ed->get_window();
+			while (w && w->get_exclusive_child()) {
+				w = w->get_exclusive_child();
+			}
+			if (w && w != this) {
+				w->add_child(this);
+				popup_centered();
+			}
+		}
+	}
+
+	void attach_and_popup_centered_ratio(float p_ratio = 0.8) {
+		EditorNode *ed = EditorNode::get_singleton();
+		if (ed && !is_inside_tree()) {
+			Window *w = ed->get_window();
+			while (w && w->get_exclusive_child()) {
+				w = w->get_exclusive_child();
+			}
+			if (w && w != this) {
+				w->add_child(this);
+				popup_centered_ratio(p_ratio);
+			}
+		}
+	}
+};
+
 void EditorNode::disambiguate_filenames(const Vector<String> p_full_paths, Vector<String> &r_filenames) {
 	ERR_FAIL_COND_MSG(p_full_paths.size() != r_filenames.size(), vformat("disambiguate_filenames requires two string vectors of same length (%d != %d).", p_full_paths.size(), r_filenames.size()));
 
@@ -615,6 +660,21 @@ void EditorNode::_notification(int p_what) {
 			if (progress_dialog) {
 				progress_dialog->queue_free();
 			}
+			if (load_error_dialog) {
+				load_error_dialog->queue_free();
+			}
+			if (execute_output_dialog) {
+				execute_output_dialog->queue_free();
+			}
+			if (warning) {
+				warning->queue_free();
+			}
+			if (accept) {
+				accept->queue_free();
+			}
+			if (save_accept) {
+				save_accept->queue_free();
+			}
 			editor_data.save_editor_external_data();
 			FileAccess::set_file_close_fail_notify_callback(nullptr);
 			log->deinit(); // Do not get messages anymore.
@@ -4266,9 +4326,11 @@ void EditorNode::add_io_error(const String &p_error) {
 
 void EditorNode::_load_error_notify(void *p_ud, const String &p_text) {
 	EditorNode *en = static_cast<EditorNode *>(p_ud);
-	en->load_errors->add_image(en->gui_base->get_theme_icon(SNAME("Error"), SNAME("EditorIcons")));
-	en->load_errors->add_text(p_text + "\n");
-	en->load_error_dialog->popup_centered_ratio(0.5);
+	if (en && en->load_error_dialog) {
+		en->load_errors->add_image(en->gui_base->get_theme_icon(SNAME("Error"), SNAME("EditorIcons")));
+		en->load_errors->add_text(p_text + "\n");
+		en->load_error_dialog->attach_and_popup_centered_ratio(0.5);
+	}
 }
 
 bool EditorNode::_find_scene_in_use(Node *p_node, const String &p_path) const {
@@ -4639,23 +4701,27 @@ Error EditorNode::export_preset(const String &p_preset, const String &p_path, bo
 
 void EditorNode::show_accept(const String &p_text, const String &p_title) {
 	current_menu_option = -1;
-	accept->set_ok_button_text(p_title);
-	accept->set_text(p_text);
-	accept->popup_centered();
+	if (accept) {
+		accept->set_ok_button_text(p_title);
+		accept->set_text(p_text);
+		accept->attach_and_popup_centered();
+	}
 }
 
 void EditorNode::show_save_accept(const String &p_text, const String &p_title) {
 	current_menu_option = -1;
-	save_accept->set_ok_button_text(p_title);
-	save_accept->set_text(p_text);
-	save_accept->popup_centered();
+	if (save_accept) {
+		save_accept->set_ok_button_text(p_title);
+		save_accept->set_text(p_text);
+		save_accept->attach_and_popup_centered();
+	}
 }
 
 void EditorNode::show_warning(const String &p_text, const String &p_title) {
-	if (warning->is_inside_tree()) {
+	if (warning) {
 		warning->set_text(p_text);
 		warning->set_title(p_title);
-		warning->popup_centered();
+		warning->attach_and_popup_centered();
 	} else {
 		WARN_PRINT(p_title + " " + p_text);
 	}
@@ -6551,11 +6617,13 @@ static void _execute_thread(void *p_ud) {
 }
 
 int EditorNode::execute_and_show_output(const String &p_title, const String &p_path, const List<String> &p_arguments, bool p_close_on_ok, bool p_close_on_errors) {
-	execute_output_dialog->set_title(p_title);
-	execute_output_dialog->get_ok_button()->set_disabled(true);
-	execute_outputs->clear();
-	execute_outputs->set_scroll_follow(true);
-	execute_output_dialog->popup_centered_ratio();
+	if (execute_output_dialog) {
+		execute_output_dialog->set_title(p_title);
+		execute_output_dialog->get_ok_button()->set_disabled(true);
+		execute_outputs->clear();
+		execute_outputs->set_scroll_follow(true);
+		execute_output_dialog->attach_and_popup_centered_ratio();
+	}
 
 	ExecuteThreadArgs eta;
 	eta.path = p_path;
@@ -6573,6 +6641,7 @@ int EditorNode::execute_and_show_output(const String &p_title, const String &p_p
 				String to_add = eta.output.substr(prev_len, eta.output.length());
 				prev_len = eta.output.length();
 				execute_outputs->add_text(to_add);
+				DisplayServer::get_singleton()->process_events(); // Get rid of pending events.
 				Main::iteration();
 			}
 		}
@@ -6582,14 +6651,16 @@ int EditorNode::execute_and_show_output(const String &p_title, const String &p_p
 	eta.execute_output_thread.wait_to_finish();
 	execute_outputs->add_text("\nExit Code: " + itos(eta.exitcode));
 
-	if (p_close_on_errors && eta.exitcode != 0) {
-		execute_output_dialog->hide();
-	}
-	if (p_close_on_ok && eta.exitcode == 0) {
-		execute_output_dialog->hide();
-	}
+	if (execute_output_dialog) {
+		if (p_close_on_errors && eta.exitcode != 0) {
+			execute_output_dialog->hide();
+		}
+		if (p_close_on_ok && eta.exitcode == 0) {
+			execute_output_dialog->hide();
+		}
 
-	execute_output_dialog->get_ok_button()->set_disabled(false);
+		execute_output_dialog->get_ok_button()->set_disabled(false);
+	}
 
 	return eta.exitcode;
 }
@@ -7160,12 +7231,10 @@ EditorNode::EditorNode() {
 	prev_scene->set_position(Point2(3, 24));
 	prev_scene->hide();
 
-	accept = memnew(AcceptDialog);
-	gui_base->add_child(accept);
+	accept = memnew(AcceptDialogAutoReparent);
 	accept->connect("confirmed", callable_mp(this, &EditorNode::_menu_confirm_current));
 
-	save_accept = memnew(AcceptDialog);
-	gui_base->add_child(save_accept);
+	save_accept = memnew(AcceptDialogAutoReparent);
 	save_accept->connect("confirmed", callable_mp(this, &EditorNode::_menu_option).bind((int)MenuOptions::FILE_SAVE_AS_SCENE));
 
 	project_export = memnew(ProjectExportDialog);
@@ -7210,9 +7279,8 @@ EditorNode::EditorNode() {
 	gui_base->add_child(fbx_importer_manager);
 #endif
 
-	warning = memnew(AcceptDialog);
+	warning = memnew(AcceptDialogAutoReparent);
 	warning->add_button(TTR("Copy Text"), true, "copy");
-	gui_base->add_child(warning);
 	warning->connect("custom_action", callable_mp(this, &EditorNode::_copy_warning));
 
 	ED_SHORTCUT("editor/next_tab", TTR("Next Scene Tab"), KeyModifierMask::CMD_OR_CTRL + Key::TAB);
@@ -7980,17 +8048,15 @@ EditorNode::EditorNode() {
 	set_process_shortcut_input(true);
 
 	load_errors = memnew(RichTextLabel);
-	load_error_dialog = memnew(AcceptDialog);
+	load_error_dialog = memnew(AcceptDialogAutoReparent);
 	load_error_dialog->add_child(load_errors);
 	load_error_dialog->set_title(TTR("Load Errors"));
-	gui_base->add_child(load_error_dialog);
 
 	execute_outputs = memnew(RichTextLabel);
 	execute_outputs->set_selection_enabled(true);
-	execute_output_dialog = memnew(AcceptDialog);
+	execute_output_dialog = memnew(AcceptDialogAutoReparent);
 	execute_output_dialog->add_child(execute_outputs);
 	execute_output_dialog->set_title("");
-	gui_base->add_child(execute_output_dialog);
 
 	EditorFileSystem::get_singleton()->connect("sources_changed", callable_mp(this, &EditorNode::_sources_changed));
 	EditorFileSystem::get_singleton()->connect("filesystem_changed", callable_mp(this, &EditorNode::_fs_changed));
diff --git a/editor/editor_node.h b/editor/editor_node.h
index 8ad5969249de..e0aea7abdeca 100644
--- a/editor/editor_node.h
+++ b/editor/editor_node.h
@@ -45,6 +45,7 @@ typedef void (*EditorPluginInitializeCallback)();
 typedef bool (*EditorBuildCallback)();
 
 class AcceptDialog;
+class AcceptDialogAutoReparent;
 class AudioStreamPreviewGenerator;
 class BackgroundProgress;
 class CenterContainer;
@@ -370,10 +371,10 @@ private:
 	PluginConfigDialog *plugin_config_dialog = nullptr;
 
 	RichTextLabel *load_errors = nullptr;
-	AcceptDialog *load_error_dialog = nullptr;
+	AcceptDialogAutoReparent *load_error_dialog = nullptr;
 
 	RichTextLabel *execute_outputs = nullptr;
-	AcceptDialog *execute_output_dialog = nullptr;
+	AcceptDialogAutoReparent *execute_output_dialog = nullptr;
 
 	Ref<Theme> theme;
 
@@ -388,10 +389,10 @@ private:
 	ConfirmationDialog *import_confirmation = nullptr;
 	ConfirmationDialog *pick_main_scene = nullptr;
 	Button *select_current_scene_button = nullptr;
-	AcceptDialog *accept = nullptr;
-	AcceptDialog *save_accept = nullptr;
+	AcceptDialogAutoReparent *accept = nullptr;
+	AcceptDialogAutoReparent *save_accept = nullptr;
 	EditorAbout *about = nullptr;
-	AcceptDialog *warning = nullptr;
+	AcceptDialogAutoReparent *warning = nullptr;
 
 	int overridden_default_layout = -1;
 	Ref<ConfigFile> default_layout;
diff --git a/editor/editor_plugin.cpp b/editor/editor_plugin.cpp
index 7b01ae69bf5a..fb2110dea37f 100644
--- a/editor/editor_plugin.cpp
+++ b/editor/editor_plugin.cpp
@@ -137,6 +137,7 @@ Vector<Ref<Texture2D>> EditorInterface::make_mesh_previews(const Vector<Ref<Mesh
 		RS::get_singleton()->instance_set_transform(light_instance2, xform * Transform3D().looking_at(Vector3(+1, -1, -2), Vector3(0, 1, 0)));
 
 		ep.step(TTR("Thumbnail..."), i);
+		DisplayServer::get_singleton()->process_events();
 		Main::iteration();
 		Main::iteration();
 		Ref<Image> img = RS::get_singleton()->texture_2d_get(viewport_texture);
diff --git a/editor/export/project_export.cpp b/editor/export/project_export.cpp
index e9ea0012bee1..a7ac95bd5b1a 100644
--- a/editor/export/project_export.cpp
+++ b/editor/export/project_export.cpp
@@ -943,8 +943,8 @@ void ProjectExportDialog::_export_pck_zip_selected(const String &p_path) {
 }
 
 void ProjectExportDialog::_open_export_template_manager() {
-	EditorNode::get_singleton()->open_export_template_manager();
 	hide();
+	EditorNode::get_singleton()->open_export_template_manager();
 }
 
 void ProjectExportDialog::_validate_export_path(const String &p_path) {
diff --git a/editor/progress_dialog.cpp b/editor/progress_dialog.cpp
index 9695a7042dae..4d76fdc99768 100644
--- a/editor/progress_dialog.cpp
+++ b/editor/progress_dialog.cpp
@@ -221,9 +221,7 @@ bool ProgressDialog::task_step(const String &p_task, const String &p_state, int
 
 	t.state->set_text(p_state);
 	last_progress_tick = OS::get_singleton()->get_ticks_usec();
-	if (cancel_hb->is_visible()) {
-		DisplayServer::get_singleton()->process_events();
-	}
+	DisplayServer::get_singleton()->process_events();
 
 #ifndef ANDROID_ENABLED
 	Main::iteration(); // this will not work on a lot of platforms, so it's only meant for the editor
diff --git a/scene/main/window.cpp b/scene/main/window.cpp
index 59e3d307c6d2..9fb4ed458feb 100644
--- a/scene/main/window.cpp
+++ b/scene/main/window.cpp
@@ -1365,8 +1365,11 @@ void Window::_window_input(const Ref<InputEvent> &p_ev) {
 
 	emit_signal(SceneStringNames::get_singleton()->window_input, p_ev);
 
-	push_input(p_ev);
-	if (!is_input_handled()) {
+	if (is_inside_tree()) {
+		push_input(p_ev);
+	}
+
+	if (!is_input_handled() && is_inside_tree()) {
 		push_unhandled_input(p_ev);
 	}
 }