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If I remember correctly what Kolenka (the calibre/PRST1 guru) said, the problem begins when you first use the SD card. The book ids in the books.db file on the SD card are supposed to be large numbers (10-digit) beginning with 4 and the internal memory book ids are low numbers starting at 0 (or 1???). The problem arises when books on the SD card are erroneously assigned a low number by the T1 and it then gets very confused.
If you can delete all the books on the SD card which have been assigned 'wrong' ids leaving at least one book with a 'correct' id then you should have no further problems as long as you don't delete the SD card books.db file.
However, I should say that I don't use an SD card so I haven't tested the above for myself.
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