Our system is running on Apache web server 2
AWS EC2 - Linux Ubuntu hosted on goDaddy
Certbot version is 0.31.0
I can login to a root shell on my machine (yes or no, or I don't know):
Yes
I'm using a control panel to manage my site (no, or provide the name and version of the control panel):
no
UPS has updated their systems and is requiring your system (applications/servers) to have their new digital certificate included in it's Trust Store, so you can communicate with them.
You need to speak with your merchant/shipping platform's customer support, only they or a forum dedicated to that can help you. This use case is far outside the scope of these forums, which are focused on using LetsEncrypt (and Certbot) to procure your own SSL certificate and configure webservers/applications with them.