Likely Causes of Missing Backlinks
If you have found any missing links through the historical data, these may be the culprits.
1. Broken Links
Broken links will very likely be caused by you. If you have made any recent changes to your link structure, whether major or minor, you need to find out the impact this action has made on your backlinks.
Because changing the link structure of pages leads to broken links, those trying to access your pages from previous links will find the pages inaccessible.
By running a backlink audit, you will find which links have disappeared because of the change. There are plugins like Broken Link Checker that discover broken or bad links and remove these links from the owner's site resulting in a loss of backlinks.
One method to forestall backlink loss is to implement 301 redirects each time you make changes to your link structure. It may not save all the links, but saving some is better than losing all.
2. Low-Quality Links
Assuming each link has a lifespan, low-quality links will have shorter life spans, and so it is with your site's backlinks; the low-quality links eventually die out or expire.
These links could have procured from a number of sources; could have been purchased by you from any PBN back then; or maybe they were spam links. Could even be that the links still exist, but to Google, they do not exist.
The bright side of this situation is that low-quality links add no SEO value to your site. These links do nothing but impact the SEO of your site in a negative way. And so it is a welcome development to see them disappear from your SEO radar.
The low-quality links will eventually die out long before the high-quality ones. So when running a backlink outreach, consider the quality of links that you procure.