### 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)

BIND_ENUM_CONSTANT(JOINT_TYPE_NONE);
	BIND_ENUM_CONSTANT(JOINT_TYPE_PIN);
	BIND_ENUM_CONSTANT(JOINT_TYPE_CONE);
	BIND_ENUM_CONSTANT(JOINT_TYPE_HINGE);
	BIND_ENUM_CONSTANT(JOINT_TYPE_SLIDER);
	BIND_ENUM_CONSTANT(JOINT_TYPE_6DOF);
}
Skeleton3D *PhysicalBone3D::find_skeleton_parent(Node *p_parent) {
	if (!p_parent) {
		return nullptr;
	}
	Skeleton3D *s = Object::cast_to<Skeleton3D>(p_parent);
	return s ? s : find_skeleton_parent(p_parent->get_parent());
}
void PhysicalBone3D::_update_joint_offset() {
	_fix_joint_offset();
	set_ignore_transform_notification(true);
	reset_to_rest_position();
	set_ignore_transform_notification(false);
#ifdef TOOLS_ENABLED
	update_gizmos();
#endif
}
void PhysicalBone3D::_fix_joint_offset() {
	// 
	if (parent_skeleton) {
		joint_offset.origin = body_offset.affine_inverse().origin;
	}
}
void PhysicalBone3D::_reload_joint() {