### 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)

switch (p_what) {
		case NOTIFICATION_ENTER_TREE:
			parent_skeleton = find_skeleton_parent(get_parent());
			update_bone_id();
			reset_to_rest_position();
			reset_physics_simulation_state();
			if (joint_data) {
				_reload_joint();
			}
			break;
		case NOTIFICATION_EXIT_TREE: {
			if (parent_skeleton) {
				if (-1 != bone_id) {
					parent_skeleton->unbind_physical_bone_from_bone(bone_id);
					bone_id = -1;
				}
			}
			parent_skeleton = nullptr;
			PhysicsServer3D::get_singleton()->joint_clear(joint);
		} break;
		case NOTIFICATION_TRANSFORM_CHANGED: {
			if (Engine::get_singleton()->is_editor_hint()) {
				update_offset();
			}
		} break;
	}
}
void PhysicalBone3D::_body_state_changed(PhysicsDirectBodyState3D *p_state) {