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Originally Posted by Marcy;
A big hassle is some books have tags hard-coded into the epubs, so I have to remove that info via Sigil, but at least you only have to do it once.
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I have never come across a case where I could not remove the tag in Calibre without resorting to Sigil.
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I would use Stanza if I could get calibre to send to it directly, like it does to iBooks.
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The reason I sometimes use Stanza is precisely because I do NOT need to download via iTunes. With Stanza I can access any book from my ebook library (around 10,000 titles) at any time and download it in a few seconds (either via WiFi or 3G) and because I use a calibre2opds generated catalog have a richly structured catalog. I have the library accessible via a web server so that Calibre does not need to be running at the time. This avoids the need to keep more than a few books on the device at a time. It is this over-the-air download capability that I wish iBooks had from a user supplied source rather than only via the apple ebook store.
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I did follow all the directions in the calibre + ipad thread. I've started opening calibre only via the command line, so I can have the debug file handy.
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I am sure that GRiker (the author of the iTunes/iPad Calibre integration will be more than happy to work with you to try and identify why your books are disappearing, and if it is a bug get it corrected.