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I think I know what is happening here. I think. I have run across this as well. You have updated the metadata for a book, in Calibre, changing the metadata, cover, etc. but when you load the book to your reader, the new data is not reflected in the book. When Calibre updates the metadata, it is not physically updated in the book, when you are done. Your reader or reading program on your computer reads the metadata from the physical book, not from Calibre. To get the correct metadata into the book so your reader can use it, you need to use one of several methods to update the book. You can use the Polish Book, Modify Epub or the Quality Check plugin. There are other ways, but I've found these are the easiest. All work on epub, which FBreader can read. You could also just convert the book and the metadata the conversion format supports, including the cover, will be updated in the new version as well.
I would suggest using the epub format, not because mobi is an older format, but because a lot of the really cool plugins work with either epub exclusively or epub and azw3. Epub is pretty close to industry standard in book publishing, followed by pdf and azw3.
Like I said above, if you convert a book, the metadata will be updated automatically, so if you convert your book to epub, you are done. If you want to stick with mobi, you will probably have to do a convert from mobi to mobi to get the metadata updated. I'm not sure which functions work with mobi since I usually work with epub, or PDF(only when there is not other choice). Hope this helps.
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