@shelbythomas No software will find all your links. A link going to your site might not even be found by Google... So just because you know it exists, doesn't mean its definitely associated with your site.
We have tons of user generated links going to our companies within The Klyne Group. We use SEM rush to run a quick backlink audit, but no software will find all your links. In fact, they often tell you that you've lost a backlink when it might still be there. So double check before you reach out to ask why they no longer link to your site.
You can use Majestic to pull in more links, but it won't really inspire more ways to get more high quality links, so there isn't much point.
Try looking at the 'links' in Google Search Console to see how many links are associated with your site.