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Originally Posted by June
OK - I just tested hooking up the 505 and opening the Sony software, which shower the 505 with my 17 collections. I then added one book to the 505 via the Sony software, ejected reader.
Plugged 505 back in and opened Calibre 0.7.4. And behold - collections are gone! 
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I am very happy to hear this. Your and JvdW's previous comments led me to finding a bug that accounts for it. Briefly, if a book was added or changed on the device outside of calibre, the calibre cache was rebuilt. This triggered a fairly obscure code path where collections were rebuilt before they had been read from the sony database. As a result, they all went away. I have fixed this bug and submitted it to Kovid.
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So the culprit seems to be using the sony software in this case.
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Yes. Copying a book onto the device or deleting a book from the device with a file manager could also trigger it.
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I ran Calibre in debug mode, do you want me to send you the file?
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Yes. But see below...
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It's still odd though that Calibre doesn't create Collections for a book that has a tag and no collection on the device (with the plugin set to 'Tags')
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Is the document a PDF? Tags aren't stored in PDFs, so calibre can't reconstruct them from the book. The bug would prevent calibre from reconstructing them from history.
If the book isn't a PDF, then yes, I would like to see the logs.