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It allows only a certain number of tags per book, but is not limited in general. I use tags for sorting too and have about 150 on my PB.
I guess the file system got confused by overwriting files which doesn't happen normally and now still sticks to the old system.
Sorry, but I don't know any help than deleting all available books via Calibre and then reformat the dic / internal memory and start from scratch. Had to do this myself once too because I messed it up.
Calibre is sometimes a bit touchy if you don't use it to add or delete books
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