From this AWS employee response on an Amazon Opsworks forum:
There isn't a way to push updates to stopped instances. We're considering ways to enable this. For now, if you create a new time or load based instance, it will get your updates.
So it would appear that for now, the only way to do what you'd like to do is to delete and recreate each of your load-based instances. This should ensure that the first time they boot up, they receive fresh versions of your custom cookbooks.