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@aritza - some years ago Kovid made a change to the algorithms that shorten and/or transliterate library file names. At the time I ended up with some books having slightly different names for different formats (e.g. 'aaa - bbb.epub' and 'aaa - bbbb.txt'). Although the anomaly was a bit disconcerting it didn't create any problems as such, and I don't recall Library check reporting any errors. But I don't recall any instances of duplicate formats with slightly different names - but our processes wouldn't be the same.
I think it was as far back as version 1.xx. IIRC when I spotted a mismatch I would drag the 'errant' format out of my file manager and drop it onto the Book Details panel, which would effectively rename the format according to the revised algorithm(s).
So my question to you is: how long have these books been in your library, and is it possible that the problem you describe has existed for a few years.
A synapse is suggesting the anomaly showed up most often in foreign language books - Irčne Némirovsky's The Wine of Solitude springs to mind.
BR
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