Saving of pickup items works.

model/save_game.gd

@@ -6,3 +6,4 @@ extends Resource
 @export var quest_states:Dictionary
 @export var player_transform:Transform3D
 @export var inventory:Array[Item]
+@export var level_pickup_items:Array[NodePath]

objects/pickup_item.gd

@@ -4,6 +4,8 @@ extends Node3D
 
 var editor_child_scene:Node3D = null
 
+signal item_picked_up(node_path:NodePath)
+
 @export var item:Item:
 	get:
 		return item
@@ -30,4 +32,5 @@ func _ready():
 func _on_area_3d_body_entered(body):
 	if body.has_method("on_item_picked_up"):
 		body.on_item_picked_up(item)
+		emit_signal("item_picked_up", get_path())
 		queue_free()

objects/pickup_item.tscn

@@ -1,7 +1,8 @@
-[gd_scene load_steps=4 format=3 uid="uid://da5r82nvypfk4"]
+[gd_scene load_steps=5 format=3 uid="uid://da5r82nvypfk4"]
 
 [ext_resource type="Script" path="res://objects/pickup_item.gd" id="1_1i8k2"]
 [ext_resource type="Resource" uid="uid://dmjr6pmb17l2y" path="res://data/items/woodplanks.tres" id="2_dph0g"]
+[ext_resource type="PackedScene" uid="uid://ysfnsrvgemi6" path="res://assets/resources/wood_planks.tscn" id="3_fvgmq"]
 
 [sub_resource type="CylinderShape3D" id="CylinderShape3D_1ndog"]
 height = 0.2
@@ -12,6 +13,8 @@ transform = Transform3D(1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0.00393829, 0)
 script = ExtResource("1_1i8k2")
 item = ExtResource("2_dph0g")
 
+[node name="Planks" type="Node3D" parent="." instance=ExtResource("3_fvgmq")]
+
 [node name="Area3D" type="Area3D" parent="."]
 
 [node name="CollisionShape3D" type="CollisionShape3D" parent="Area3D"]

root_ui.gd

@@ -53,6 +53,9 @@ func load_scene(scene_resource:PackedScene):
 	scene.add_child(scene_resource.instantiate())
 	current_level_resource = scene_resource.resource_path
 	
+	for pickup_item in get_tree().get_nodes_in_group("pickup_item"):
+		pickup_item.connect("item_picked_up", get_parent().on_item_pickup)
+	
 	_player = scene.find_child("Player", true, false)
 
 	if _player:

scenes/game.tscn

@@ -124,5 +124,3 @@ script = ExtResource("14_g3xjj")
 
 [node name="ScaredToWalkInTheDark" type="Node" parent="Quests" groups=["quest_state"]]
 script = ExtResource("18_7v3bk")
-
-[connection signal="visibility_changed" from="." to="." method="_on_visibility_changed"]

scenes/main.gd

@@ -6,6 +6,8 @@ extends Node3D
 
 @onready var root_ui:RootUI = %RootUI
 
+var _picked_up_level_items:Array[NodePath] = []
+
 func save_game():
 	var player:Player = find_child("Player", true, false)
 
@@ -16,6 +18,7 @@ func save_game():
 	var save_game:SaveGame = SaveGame.new()
 	
 	save_game.level = root_ui.current_level_resource
+	save_game.level_pickup_items = _picked_up_level_items
 	save_game.player_transform = player.global_transform
 	
 	for node:Node in get_tree().get_nodes_in_group("quest_state"):
@@ -32,6 +35,8 @@ func save_game():
 	root_ui.activate_ui_panel(%GameUI)
 
 func load_game():
+	_picked_up_level_items.clear()
+	
 	var save_game:SaveGame = load("user://savegame.tres") as SaveGame
 	var level_resource:PackedScene = load(save_game.level)
 	root_ui.load_scene(level_resource)
@@ -44,14 +49,25 @@ func load_game():
 
 	player.global_transform = save_game.player_transform
 	
+	# Quest state
 	for node:Node in get_tree().get_nodes_in_group("quest_state"):
 		for property in node.get_property_list():
 			if (property.usage & PROPERTY_USAGE_STORAGE != 0) and (property.usage & PROPERTY_USAGE_SCRIPT_VARIABLE) != 0:
 				node.set(property.name, save_game.quest_states[node.name][property.name])
 	
+	# Inventory
 	player.inventory.clear()
 	for item in save_game.inventory:
 		player.inventory.add_item(item)
 	
+	# Picked up items
+	for item_path in save_game.level_pickup_items:
+		if get_tree().root.has_node(item_path):
+			var item_node = get_tree().root.get_node(item_path)
+			_picked_up_level_items.append(item_path)
+			item_node.queue_free()
+	
 	root_ui.activate_ui_panel(%GameUI)
 
+func on_item_pickup(node_path:NodePath):
+	_picked_up_level_items.append(node_path)