This script allows you to delete all the tweets in a twitter account using twython library. You have to first download the twitter history archive and then extract the downloaded folder. All the information regarding the tweets can be found in "tweet.js" file. This file can easly be read and manipulated using python.

delete_tweets.py

import re
from twython import Twython
import sys

# authorization info of your app
auth = {'APP_KEY':'',
        'APP_SECRET':'',
        'OAUTH_TOKEN':'',
        'OAUTH_TOKEN_SECRET':'',
        'SCREEN_NAME':'',
        'keywords':[],
        'users':['']}

#get from twitter developer site
APP_KEY = auth['APP_KEY']
APP_SECRET = auth['APP_SECRET']
TOKEN = auth['OAUTH_TOKEN']
TOKEN_SECRET = auth['OAUTH_TOKEN_SECRET']

# instance creation
twitter = Twython(APP_KEY, APP_SECRET, TOKEN, TOKEN_SECRET)


# tweet.js file should be in the same path of this script
id_list = []
for line in open("tweet.js", "r").readlines():
  if '"id"' in str(line):
    tmp = str(line).replace('"id" : ','')
    id_list.append(re.findall('"([^"]*)"', tmp)[0])
    
for id in id_list:
  try:
    twitter.destroy_status(id=id)
  except:
    None