I've had great success using StarOffice 8.0 (the Sun version of OpenOffice.org) to create my ebooks. I take the source document, save it as an OpenDocument text file, format the OpenDocument file for the Sony Reader (I set the page size to 3.5" x 4.75" with 0.2" margins), and then export it as a PDF.
As long as StarOffice/OpenOffice.org (SO/OO.o) can open the original file, or you can convert the file into a format that SO/OO.o can read, you should have little trouble creating a PDF from the document. Unfortunately, I checked the list of formats that it can open, and .indd isn't listed. I'm not familiar with the extension, so I don't know if an .indd file can be converted into a format that is compatible with SO/OO.o.
I hope that helps.
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