### Godot version

Godot 4 stable and Godot 3.x LTS

### System information

Fedora linux

### Issue description

If you use some custom logic inside _integrate_forces() to alter the state linear velocity and there is any reference to linear_velocity in physics process, the result in godot 3.5 is that it moves just a little bit, while in godot 4 is totally still.

### Steps to reproduce

For the example i created a simple scene in which i apply a force on the linear velocity in  _integrate_forces()  and added a line that add zero to it in physics process. You will not see any move, but it will work fine if you comment the line adding zero.


### Minimal reproduction project

[PhysicsBugReproduction.zip](https://github.com/godotengine/godot/files/12139772/PhysicsBugReproduction.zip)

if (!parent_skeleton) {
		return;
	}
	if (parent_skeleton->get_animate_physical_bones()) {
		set_body_mode(PhysicsServer3D::BODY_MODE_KINEMATIC);
		PhysicsServer3D::get_singleton()->body_set_collision_layer(get_rid(), get_collision_layer());
		PhysicsServer3D::get_singleton()->body_set_collision_mask(get_rid(), get_collision_mask());
		PhysicsServer3D::get_singleton()->body_set_collision_priority(get_rid(), get_collision_priority());
	} else {
		set_body_mode(PhysicsServer3D::BODY_MODE_STATIC);
		PhysicsServer3D::get_singleton()->body_set_collision_layer(get_rid(), 0);
		PhysicsServer3D::get_singleton()->body_set_collision_mask(get_rid(), 0);
		PhysicsServer3D::get_singleton()->body_set_collision_priority(get_rid(), 1.0);
	}
	if (_internal_simulate_physics) {
		PhysicsServer3D::get_singleton()->body_set_state_sync_callback(get_rid(), Callable());
		parent_skeleton->set_bone_global_pose_override(bone_id, Transform3D(), 0.0, false);
		set_as_top_level(false);
		_internal_simulate_physics = false;
	}
}