The lines:

for fn ∈ os.listdir(targets_dir):
    if os.stat(os.path.join(targets_dir, fn)).st_ino == target_ino:
        prefixes.append(fn)

from build_docs.py are searching all the http-exposed directories pointing to the currently build directory. It's building a wrong list of directories, not being able to spot he's in a subdirectory:

• target is /srv/docs.python.org/fr/3.5
• so targets_dir is /srv/docs.python.org/fr
• the os.listdir will get the right list of translated versions
• prefixes will only contain the versions like ['3.6'] not ['fr/3.6']
• so to_purge will contain something like ['3.5', '3.5/about.html'] missing the fr/ prefix.