The SEF URLs in JOOMLA stopped working

Hears,
SEMrush

I am currently hosting several Joomla sites on an Ubuntu 16.04 LTS LAMP server. I am using Joomla 3.9, Apache / 2.4.37, PHP 7.1 and MySQL. We recently configured SEF URLS through Joomla successfully.

However, yesterday I was doing updates / updates on the web server specifically PHP from 7.0 to 7.1 by following this article here:

https://jakelprice.com/article/how-to-u … -to-php-71

During this update to PHP 7.1, there also seemed to be some updates for APACHE now it seems that all our SEF URLs that were working no longer work and give an error:

Lost
The URL / requested government relations was not found on this server.

I followed the same steps we had when we were successful, but it still does not work. Any help would be greatly appreciated.