I believe that both Flow and TypeScript are competing solutions that are precursors to what may eventually become standard in JavaScript. At that point, all the annotations written for Flow and TypeScript will become obsolete overnight.
This is essentially the same thing that happened to AMD, and one of the reasons that I advocated for users to chose Node-style modules and Browserify (and now Webpack) instead of AMD.
I consulted on several projects and gave exactly that advice. They didn't listen. Now they're stuck supporting a huge AMD legacy & Bower ecosystem and the authors of Bower are no longer supporting it.
That is the future that awaits those who build TypeScript + Flow-annotated applications. Fine if it's just a few modules here and there, but for large enterprise apps, you're building a mountain of technical debt what will eventually need to be paid.
Don't get me wrong, I am really excited that Flow and TypeScript are paving the way, and I blatantly stole some good ideas from them for rtype/rfx, but I'm also very wary about leading people down a road that I am pretty confident will dead-end within a few years.
Both projects still have great value though. We learned a lot from AMD, and it has influenced the new standards. I am confident that TypeScript and Flow with both influence whatever we get in the JS standard. I know the TypeScript team is already experimenting with additions to the runtime reflection specifications coming in future iterations of ECMAScript.