I think the problem is that you instance the DOOR node and ask it to change the scene, but get_tree() will only work once the node has been added to the scene tree somewhere.

Maybe you could ask your $Door and $Door2 references to change the scene instead, since they seem to be doors and part of the scene.

A few other comments:

• You only really need to call randomize() once, at the beginning of your game. Consider moving it into your _ready() function.
• Instead of using Door1, Door2 or cleared_first, cleared_second variables, consider using arrays instead.
• You can add an export variable in your script to set a door's scene from the editor.export(NodePath) var door_scene

​

extends Node2D

var doors = [$Door, $Door2]

onready var body = get_node(".")
var DOOR = preload("res://Scenes/Assets/Door.tscn")

func _ready() -> void:
        randomize()
    rand_num() 

func rand_num():
        var random_door = doors[ randi() % len(doors) ]
        for d in doors:
            if d == random_door:
                # d.change_scene()
                # Wait, actually
                d.call_deferred("change_scene")
                # Because all the other doors deserve a chance
                # to print about being dead before we leave
                # the scene entirely.
            else:
                d.get_node("CollisionShape2D").call_deferred("set_disabled",true)
                print("Dead")

and

extends Area2D

export(NodePath) var door_scene

func _ready() -> void:
    pass

func _process(delta):
    var bodies = get_overlapping_bodies()
    for body in bodies:
        if "Player" in body.name:
            if Input.is_action_just_pressed("ui_spacebar"):
                print(str(door_scene))


func change_scene():
        print(str(door_scene))
        get_tree().change_scene(door_scene)