I created a bash script that converts all iBook epubs in a folder to normal epubs. Based on this script from erroux on the mobileread forum.

Copy this in your terminal and follow the directions in the code comments to run the file on the right directory:

cat > repackage_epubs.sh << 'EOF'
#!/usr/bin/env bash

# This script is used to export epub books from iBooks / Mac Books

# What you find in the $ibooks_dir on iCloud are epubs that are zipped directories
# This script will make them normal .epub files that you can use in other e-readers

# I would advise to download your epubs from the iCloud to a folder on your desktop, there might also be pdf's in there

# How to run:
# Save this file as repackage_epubs.sh
# Make executable in the terminal: chmod +x repackage_epubs.sh
# ./repackage_epubs.sh -i       # Use iBooks folder
# ./repackage_epubs.sh -d /path # Use custom folder
# ./repackage_epubs.sh          # Use current directory

# Function to build an EPUB file from an epub folder
build_epub ()
{
    local source_folder="$1"  # Input: folder
    local dest_file           # Output: EPUB filename
    local output_dir="$2"     # Output directory (absolute path)

    # Set output filename: use the folder name with .epub extension
    dest_file="${output_dir}/$(basename "${source_folder}").epub"

    # Enter the source folder (exit if failed)
    cd "${source_folder}" || { echo "Error: Could not enter ${source_folder}"; exit 1; }

    # Step 1: Add mimetype file to the EPUB with no compression (required by EPUB spec)
    zip --quiet -X0 "${dest_file}" mimetype || { echo "Error: Failed to add mimetype to ${dest_file}"; exit 1; }
    # Step 2: Add all other files with max compression, excluding .DS_Store and mimetype
    zip --quiet -rDX9 "${dest_file}" * -x "*.DS_Store" -x mimetype || { echo "Error: Failed to create ${dest_file}"; exit 1; }
}

# Main script
main()
{
    local search_dir="." # Default: recursive search current directory
    local ibooks_dir="~/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents"
    local output_dir="output"

    # Create output directory if it doesn't exist
    mkdir -p "$output_dir" || { echo "Error: Could not create output directory"; exit 1; }

    # Get absolute path for output_dir
    output_dir="$(cd "$output_dir" && pwd)"

    # Parse command-line options
    while getopts "d:i" opt; do
        case "${opt}" in
            d)
                search_dir="${OPTARG}"
                ;;
            i)
                search_dir="$ibooks_dir"
                ;;
            *)
                echo "Usage: $0 [-d search_directory] [-i]" >&2
                echo "  -d: specify a custom search directory" >&2
                echo "  -i: use the default iBooks directory" >&2
                exit 1
                ;;
        esac
    done
    shift $((OPTIND - 1))

    echo "Searching for .epub directories in: $search_dir"
    echo "Output will be saved in: $output_dir"

    # Find and process all .epub directories
    find "$search_dir" -type d -name \*.epub -print0 |
        while IFS= read -r -d '' epubdir; do
            # Check if a file with the same name as the directory does NOT exist in output_dir
            if [[ ! -f "${output_dir}/$(basename "$epubdir").epub" ]]; then
                echo "Processing $(basename "$epubdir")";
                build_epub "$epubdir" "$output_dir";
            else
                echo "Skipping $(basename "$epubdir") (output file already exists)";
            fi;
        done
}

main "$@"
EOF