A press release crossed my inbox earlier this week promoting new conversion service. Circular Software can now take an inDesign file and output an Epub in Apple's fixed layout format. It's a little expensive, but it's the first automated option that I have heard of.
I know of a handful of ebook conversion specialists who could probably offer a similar service, but it's still fairly rare. Also, of all the common ebook formats, fixed layout Epub was the one that (so far as I knew) still had to be done by hand. An automated option is a big step forward.
But here's the bad news; they're asking a $200 fee for each Epub converted.
That's rather expensive for an automated service, but then again Circular has the market to themselves largely to themselves. To be honest, I'm not sure who else offers this service. I believe Red Staple can do it, but I couldn't get a confirmation from them.
P.S. If anyone knows of a cheaper alternative, please let me know.