Thanks Mitchell!
I wonder if I can write the letsencrypt commands into a second bash script, then make the original bash script copy over the second script to the correct directory and initiate the script to run. I’ll do some testing and see if that works 
So am I right in thinking that any certonly command (inside or outside a bash script) such as:
letsencrypt certonly -a webroot --webroot-path=/var/www/html --agree-tos --email example@example.com -d example.com
Should be run from /etc/letsencrypt/ and can not be run from any other directory or else the renewal config will be incorrect? I feel like I’m missing something. Maybe this only applies when running the commands from a bash script?
Thanks again!
Jamie.