Yes, you can check your links (using whatever tool) to find out what is indexed/deindexed. But it's more likely your site's usefulness to visitors got 'voted down' by Google compared to other sites. The listing on page 1-2 of the search engines is a 'beauty contest' line-up of finalists---you have to keep finding a way to stand out to win the pageant. Good linking gets it ranked, but you have to satisfy the visitors once there, to keep it ranked.
Check what engagement elements competitors are using, and try to stay even with them. Add longer content, more videos, images, giveaways, infuencer roundups, etc. Offer a free ebook you mention on the home page or key pages, but make visitors have to click a link to a download page elsewhere on the site (Google will count the inner page clickthroughs as evidence of better dwell time on the site, thus better engagement). Etc, etc.