Ah, then there is definitely a dataloss bug. From my orig. message: I have a 200 page PDF that is a combination of multiple smaller PDFs. The PDF that Calibre sends to the device only contains the first of these smaller PDFs, i.e., 15 pages, not the full 200 page ebook. I can send the full ebook somewhere if you want to try to reproduce the bug; it's 7MB.
I wonder what makes setting PDF metadata so slow. Does Calibre first send the copy to the device, and then modify the metadata on the device? It might be faster to modify a local copy, then to send that.