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A runtime check would make a library inaccessible, when, as you correctly point out, only a few books in the library might suffer from the actual issue. As a user I certainly would not like being suddenly unable to access my library in calibre because I moved the library folder.
Placing calibre libraries deep inside folder hierarchies on windows is simply not a good idea, and is not something I wish to encourage. As for including it in your suite of programs you can do so by simply installing it into a temp directory and moving it after install. Though again, I certainly dont recommend that you do that, because it will mean things will break for you r users if they use books with long titles/authors.
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