Can be used to flush the rewrite rules of all sites in a multisite network.

flush-permalink.sh

#!/bin/bash
# Delete the rewrite_rules of every blog and ping them to recreate the rewrite rules.
#
# Assumptions:
# 1. Your database prefix is wp_
# 2. Your sites are using https://
# 3. The mysql credentials specifed in your .cnf file have the approriate permissions (obviously)
#
# Usage: ./report-all-blog-themes.sh /path/to/mysql.cnf
set -e

for DATABASE in $(mysql --defaults-extra-file=$1 --skip-column-names -e "SHOW databases;" --batch); do
    IS_MULTISITE=$(mysql --defaults-extra-file=$1 --skip-column-names -e "SHOW TABLES FROM $DATABASE LIKE 'wp_site';" --batch)
    if [ '' == "$IS_MULTISITE" ]; then
    	continue
    fi
    for BLOG_ID in $(mysql --defaults-extra-file=$1 -e "SELECT blog_id FROM wp_blogs;" "$DATABASE" --batch --skip-column-names); do
        URL=$(mysql --defaults-extra-file=$1 -e "SELECT concat( 'https://', domain, path ) AS URL FROM wp_blogs WHERE blog_id = ${BLOG_ID}" $DATABASE)
        echo $BLOG_ID - $URL;
        mysql --defaults-extra-file=$1 ${DATABASE} -e "DELETE FROM wp_${BLOG_ID}_options WHERE wp_${BLOG_ID}_options.option_name=\"rewrite_rules\";";
        curl -I ${URL}
    done
done

exit 0

Have you used wp-cli ?

https://wp-cli.org/commands/rewrite/flush/