Unless you're able to crack how the .story files are constructed (they are HTML IiIRC) there is no way that I am aware of.
The last time I had to update a Captivate project in Articulate, I used Camtasia to capture my screen as I completed the e-learning.
Then I split the video up into "slide-sized" bits and remade the slides that required updates. The rest I left as a video on each Storyline slide.
It wasn't a pretty process and the result wasn't fantastic. But I got the Flash stuff recorded in a fair condition.
I have no idea if you can go from Storyline to Captivate in any better way. But I'd rather step on glass shards and rusty nails barefoot than use Captivate again- I would at least consider doing it if I had a choice.
