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1. Have you checked the metadata in calibre (namely: Language)? If yes, you might also have a look into the book code (.css files): sometimes language can be hardcoded in there. For the other error I don't know, I think only the dev might help you with that
2. Not that I know, you shall remove it by hand. But I am not sure what you mean by "hard-coded" hypenation... you see the li-ne-s wro-te as this e-ven the-y do not break? If not, I wouldn't say it is hard-hypenated...
3. I don't think Calibre is scriptable, but you may run each step for the whole bunch of books, you just need to select all the books in advance and run the action you need
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