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Originally Posted by twedigteam
We're in the same boat, just working through a large library of ePub files, converting to MobiPocket. @random43743 we'd like to share your experience with using either the KindleGen or Calibre. I'm also wondering if creating Mobi files from scratch is doable + worht the time.
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It's certainly doable, but would involve creating essentially the same files that you already have in the EPUB file (XHTML content, CSS file, images, and XML .opf and .ncx files). An EPUB file simply bundles these files (plus an additional "mimetype" file) in a zip archive, whereas a MOBI file bundles them up in a proprietary format. MOBI is also more limited in the formatting options that will work successfully.
If your intention is to publish the MOBI files on Amazon for sale in the Kindle store, I'd recommend using Kindlegen to convert the EPUB files (one reason being that there is a problem with Amazon DRM, Calibre-created MOBI files, and the Kindle for PC application). Otherwise you could try a few with each application and use the one that gives the best conversion results.