Below is a bash script to recursively sanitize folder and file names. It leaves all numbers, letters, dots, hyphens and underscores untouched, but replaces all other characters with underscores.

#! /bin/bash

sanitize() {
  shopt -s extglob;

  filename=$(basename "$1")
  directory=$(dirname "$1")

  filename_clean="${filename//+([^[:alnum:]_-\.])/_}"

  if (test "$filename" != "$filename_clean")
  then
    mv -v --backup=numbered "$1" "$directory/$filename_clean"
  fi
}

export -f sanitize
find $1 -depth -exec bash -c 'sanitize "$0"' {} \;