#!/bin/bash
s='aaaaa,bbbbb,"ccc,ccc","ddd,ddd,ddd",eee'
perl -pe 's{"[^"]+"}{$&=~s/,/_/gr}ge' <<< "$s"
sed 's/"[^"]*"/\n&/g;:a;s/\(\n"[^"]*\),/\1_/g;ta;s/\n//g' <<< "$s"
IyEvYmluL2Jhc2gKCnM9J2FhYWFhLGJiYmJiLCJjY2MsY2NjIiwiZGRkLGRkZCxkZGQiLGVlZScKCnBlcmwgLXBlICdzeyJbXiJdKyJ9eyQmPX5zLywvXy9ncn1nZScgPDw8ICIkcyIKCnNlZCAncy8iW14iXSoiL1xuJi9nOzphO3MvXChcbiJbXiJdKlwpLC9cMV8vZzt0YTtzL1xuLy9nJyA8PDwgIiRzIg==