update.py

with open(config.get_deposition_file()) as f:
    deposition_id = f.read()

# create a new deposition version with different deposition_id from the existing deposition
r = requests.post(config.url + '/api/deposit/depositions/' + deposition_id + '/actions/newversion',
                  params={'access_token': config.access_token})

# You have to use the new version's deposit link
newversion_draft_url = r.json()['links']['latest_draft']

# There is a new "deposition_id" now:
deposition_id = newversion_draft_url.split('/')[-1]  # Extract deposition_id from url

################## ACTIONS ####################
# 2. upload a new file to this existing deposition
data = {'filename': config.file_name_to_upload}
files = {'file': open(file_path_to_upload, 'rb')}
r = requests.post(newversion_draft_url + '/files',  # <--- Notice the use of the new link
                  params={'access_token': config.access_token}, data=data,
                  files=files)
print r