I just experienced a similar problem (collections lost, as well as all bookmarks for books in collections, though books themselves are intact), but I doubt that lack of storage was the issue.
I transferred the following books to my Reader's 1 GB SD card, all in a group (and all from this forum, downloaded today, 5-21-07):
Autobiography of Benjamin Franklin
Isildur
The Charge of the Light Brigade (v1,1)
Treasure Island v2
The Haunted Bookshop
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War of the Worlds
Good-Bye, Mr. Chips
...and after paging around in my new acquisitions I went to reset the reader to my last bookmark in Blue Mars (from the Collect store), and found that its bookmark was missing from the list. A little checking, and the extent of the data loss became clear, as mentioned above.
I did notice that after unplugging the USB cable this time it seemed like the Reader went through four "spinning arrow" cycles (as opposed to its usual two) before releasing me to the main menu, as though it had had to recover from something.
Does anyone know what might have triggered the problem? I'm pretty careful to either click the "eject" icon in Connect, or close Connect, before disconnecting the Reader (though who knows, I might have forgotten this time).
-Rich
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