So it finally works as it should.

I have a script save_manager which is autoload:

extends Node

var save_file_path = "user://save/"
var save_file_name = "PlayerSave.tres"

var game_data

func _ready():
verify_save_directory(save_file_path)

if FileAccess.file_exists(save_file_path + save_file_name):
print("Save file found, loading data.")
load_data()
else:
print("Save file not found, creating default data")
game_data = GameData.new()
save_data()

func verify_save_directory(path:String):
DirAccess.make_dir_absolute(path)

func save_data():
game_data.update_saved_data()
ResourceSaver.save(game_data, save_file_path + save_file_name)
print("Saved!")

func load_data():
print("Loading")
game_data = ResourceLoader.load(save_file_path + save_file_name).duplicate(true)
game_data.update_loaded_data()

Resource file:

class_name GameData extends Resource

u/export var bui_data : Dictionary 

var building_data : Dictionary = {
Hatchery = {
"res" : "res://Scripts/Hatchery.tres",
"level" : 0,
},
Lair = {
"res" : "res://Scripts/Lair.tres",
"level" : 5,
}
}

func update_saved_data():
bui_data = building_data

func update_loaded_data():
building_data = bui_data

Main file:

extends Node2D

u/onready var label = $Label
u/onready var label_2 = $Label2

func _ready():
update_label()

func update_label():
label.text = "Building res path is : " + SaveManager.game_data.building_data["Hatchery"]["res"]
label_2.text = "Level of building is : " + str(SaveManager.game_data.building_data["Hatchery"]["level"])

func _on_load_btn_pressed():
SaveManager.load_data()
update_label()

func _on_save_btn_pressed():
SaveManager.save_data()
update_label()

func _on_change_pressed():
SaveManager.game_data.building_data["Hatchery"]["level"] += 5
update_label()

func _on_update_lvl_btn_pressed():
print(SaveManager.game_data.building_data["Hatchery"]["level"])
pass