Calibre on Linux doesn't write out the file names properly because they are paranoid that you might try to move it to an operating system that doesn't support those characters.

Calibre Fix Save To Disk File Names

#!/bin/bash
#shellcheck shell=bash

# Requires unzip and xmlstarlet

# Assumes that you are extracting metadata as well, though you could extract
# the opf from the epub at run time but I don't know how to do this for other
# formats

# I also only get the first author because I didn't want to deal with adding
# '&' or ',' or ', and' for each author, and determing when each is appropriate

# Assumes you want a format of 'Author Name/Book Name/Book Name.extension'
# But it wouldn't take much to change it to whatever format you want

basedir="$1"
basedir="$(readlink -f "$basedir")"
if [[ ! -d "$basedir" ]]; then
    echo "$basedir was not found or is inaccessible!"
    exit 1
fi

mapfile -t books < <(find "$basedir" -type f -name '*.opf')
for book in "${books[@]}"; do 
    dname="$(dirname "$book")"
    title="$(xmlstarlet sel -N  opf="http://www.idpf.org/2007/opf" \
        -N dc="http://purl.org/dc/elements/1.1/"  -t -m \
        '/opf:package/opf:metadata/dc:title' -v . -n "$book")"
    mapfile -t authors < <(xmlstarlet sel -N  \
        opf="http://www.idpf.org/2007/opf"  \
        -N dc="http://purl.org/dc/elements/1.1/" -t -m \
        '/opf:package/opf:metadata/dc:creator' -v . -n "$book")
    author="${authors[0]}"
    # Fix the filenames of the exported files
    mapfile -t book_files < <(find "$dname" -type f)
    for book_file in "${book_files[@]}"; do
        bname="$(basename "$book_file")"
        dname="$(dirname "$book_file")"
        fname="${bname%%\.*}"
        extension="${book_file##*\.}"
        if [[ "$fname" != "$title" ]]; then
            mv "${book_file}" "${dname}/${title}.${extension}"
        fi
    done
    # Fix the title directory if it's different
    title_dir="$(dirname "$book")"
    title_dir_dname="$(dirname "$title_dir")"
    title_dir_name="$(basename "$title_dir" )"
    if [[ "$title_dir_name" != "$title" ]]; then
        mv "$title_dir" "${title_dir_dname}/${title}"
    fi
    # Fix the author directory if it's different
    author_dir="$(dirname "$title_dir")"
    author_dir_dname="$(dirname "$author_dir")"
    author_dir_name="$(basename "$author_dir" )"
    if [[ "$author_dir_name" != "$author" ]]; then
        mv "$author_dir" "${author_dir_dname}/${author}"
    fi
done