sweet @schoen sounds like a great improvement 
But I was referring to re-running the same commands again as in these that setup the actual /etc/letsencrypt directory and structure initially. If these where re-ran, would they override or wipe existing contents in /etc/letsencrypt. Sorry for not clarifying my question
virtualenv --no-site-packages -p python2 venv
./venv/bin/pip install -r requirements.txt acme/ . letsencrypt-apache/ letsencrypt-nginx/