How to update Certbot version?

sudo apt update
sudo apt install --only-upgrade certbot

Tried it on ubuntu with nginx, worked for me without issues.

Not sure how I missed this. From the install docs https://certbot.eff.org/docs/install.html#certbot-auto

user@webserver:~$ wget https://dl.eff.org/certbot-auto
user@webserver:~$ chmod a+x ./certbot-auto
user@webserver:~$ ./certbot-auto --help

You can check for your software version but this works:

sudo apt-get update -y
sudo apt-get install software-properties-common
sudo add-apt-repository universe
sudo add-apt-repository ppa:certbot/certbot
sudo apt-get update -y
sudo apt-get install certbot python-certbot-apache
certbot --version

https://certbot.eff.org/lets-encrypt/ubuntuxenial-apache