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1) Umm why would the book not be intact? If you are worried about data on your disk being randomly corrupted, you have bigger problems. By that logic, any file on your disk that is changed by any program at any time could possibly be corrupt and need restoring from backups.
2) Exact binary matches of ebooks are pretty useless, unless they are the exact same file, in which case, they will also match on lots of other dimensions, not affected by the presence of a bookmarks file.
3) Since the bookmarks are file specific, replacing the epub file with another means the bookmarks wont work anyway.
4) Since you are reading the books in the viewer and the viewer internally converts all formats to an epub like format anyway, it doesn't matter if you prefer reading another format, you are effectively reading epub in any case.
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