How to load game without entity stack with preset entity in scene?

Godot Version

4.3

Question

i make new map scene with entity like ( box ( can be break) ) in it.
when i run new game ,all box is set in map as i preset.
when i save the game. then load back
all box from load data and preset is stack.

eg. if i destroyed box when i first enter game. then load. all box that i preset will be in map. and no more box from load( because i destroyed and load).

so , how to make when i load a game all preset entity is remove , only insta from load data?

as for now, what im doing is when load game,
1 - load the map , then remove “queue_free” all preset entity.
2 - then load entity from load data.

so how should i load without need to queue_free then load entity.
should i make new map scene without any entity in it? the switch between the map with entity and without entity in it? , if i do like that i need to do to all map i have.
there a way to make easy to handle it?