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OK I removed all the books from my internal memory and all the Collections. Then disconnected. Ensured the device was empty except for the Users Guide.
Reconnected and copied 84 books back to the Reader. Disconnected. The T1 removed all the books from the Collections, but left the Collections (although they were all empty).
Reconnected and added a few more books. Disconnected and again the T1 removed these from the Collections. Leaving all empty Collections. This time however there were no duplicate Collections created.
The original books were in a directory on the internal memory under the calibre directory and then sub-directories by author. They were created by the first beta. The new ones are in the default directory. Therefore I suspect that this different directory locations may have something to do with the duplicate Collections that were occurring.
One other weirdness, when I reconnected just now about 40 books are checked as Main in the Library view and these same books are checked as In Library in the Device view. That leaves about 47 books that are also displayed in the Device view and are on the T1, but are not shown as matching in the Device or Library views within Calibre.
So now it looks like the three main bugs are:
1. Why is the SD card not showing up in Calibre?
2. Why is the T1 erasing the books in the Collections after disconnecting from the computer (while leaving the books and empty Collections)?
3. Why are some of the books not matching between the Library and Device views but are on the T1 and in the Device view?
HTH
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