There is nothing like success, and every skunk works has to produce it. Whenever you succeed, take the opportunity to tell the story of how this would not have been possible without the organization behind it. Equally important, build the body of evidence that shows a return to the institution on the investment it has made. Once you're able to show that equation, you're almost there. In my case, by the time we entered our third year, even the most skeptical bystanders and adversaries admitted that our results were worth the effort.
People move on.
Sponsors desert you. For a skunk works to live on and continue its contribution, it has to adapt and evolve. In most cases, this is not a function of process but one of people and identity. If enough of your people have the fire of innovation lit inside them, they will attract others and the organization will stay alive. This recipe takes a bit of work, but it's worth it when you're finished.