What do you have "Metadata management" set to on the "Sending books to devices" page of the calibre preferences? It sounds like you have it set to automatic. Using automatic, the current driver will reset the reading status of all books except the ones with the tags "Im_Reading", "Read" or "Closed". And it will reset the shortlist unless the book has the tag "Shortlist". If you don't want this to happen, change this option to "manual".
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