Activating Yoast Canonical URL with PHP

I have a site where we had previously installed and activated the SEO no Duplicate plugin for WP. This canonical plugin overrides the YOAST SEO canonical element and allows you to customize one. Well, we can do that with YOAST so I choose to remove the old canonical plugin and start using the one provided by Yoast SEO.

However, I think that there was custom work added by the previous developer that shut off the YOAST canonical so when I add a URL to YOAST canonical and view the source code afterwards, it does not display. There is nowhere to find it. It is not activated but the YOAST plugin is. I looked in YOAST settings to find where I can turn it on and shut it off but I cold not find it.

Is there a code in the functions.php file where I can find a way to turn it on and off? and what type of code should I look out for? I keep searching but I cannot find a solution. I have another site where this is working correctly so something in this initial site made it shut off.

If you know of a short code that could help me turn it on please feel free to help out, most of the articles I looked at where custom request in nature so they didn't answer my question.