### 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)

return angular_velocity;
}
void PhysicalBone3D::set_use_custom_integrator(bool p_enable) {
	if (custom_integrator == p_enable) {
		return;
	}
	custom_integrator = p_enable;
	PhysicsServer3D::get_singleton()->body_set_omit_force_integration(get_rid(), p_enable);
}
bool PhysicalBone3D::is_using_custom_integrator() {
	return custom_integrator;
}
void PhysicalBone3D::reset_physics_simulation_state() {
	if (simulate_physics) {
		_start_physics_simulation();
	} else {
		_stop_physics_simulation();
	}
}
void PhysicalBone3D::reset_to_rest_position() {
	if (parent_skeleton) {
		if (-1 == bone_id) {
			set_global_transform(parent_skeleton->get_global_transform() * body_offset);
		} else {
			set_global_transform(parent_skeleton->get_global_transform() * parent_skeleton->get_bone_global_pose(bone_id) * body_offset);
		}
	}
}
bool PhysicalBone3D::PinJointData::_set(const StringName &p_name, const Variant &p_value, RID j) {