Google's John Mueller provided some advice on a site that seemed to have been hit due to bad links. He said on Mastodon, "If you've built the foundation of your site on bad links for a longer period of time, that will have a lasting effect even if you suddenly fix some things."
John then gave this analogy, "It's tempting to build a house out of cardboard, it's cheap & it looks like a house quickly. Removing the cardboard doesn't make it a stable house."
It is a concept many SEOs (not you, other SEOs) don't seem to get. If Google stops crediting these links to your site, they stop working - the deck of cards you built up will collapse. Those links are no longer holding up the site because Google "neutralized" them. Using a disavow file doesn't do anything but the disavow file does the same thing as the algorithm did, it will neutralize the links.
John said earlier in that thread, "For algorithmic effects, your changes will be taken into account over time (though it might take a lot of time, so fix it right & for good)."
Here is a screenshot of this thread:
Forum discussion at Mastodon.
