In the beginning of December 2015, Search Engine Roundtable reported a case of a person removing all of the backlinks in their disavow file and then stating that they saw a huge rankings boost as a result of this.
Of course, we know the SEO world we live in, so there were most certainly other factors involved as well, but it wasn’t the first time this exact same scenario has been discussed.
In one of the last Google Hangouts for 2015 (around 30:35), John Mueller from Google was asked whether it is okay to do exactly that or are you simply exposing yourself for the spammer that you are. Basically John was questioned whether you can safely remove, in bulk, backlinks from your disavow file:
If a great number of URLs (more than 1000 URLs and 1000 domains) was removed from [a] Disavow file, can it be called a link boom? For example, if the URLs were added by mistake more than half a year ago?
Mueller responded with a negative, confirming that you can do whatever you want and that this action is simply a technical change which doesn’t necessarily result in a manual review:
I don’t see any problem with that. That is not something where I would say this would be a bad thing or a good thing. It is essentially just a technical change that you are making, you are telling us when we re-crawl those URLs we should take those links into count. And if those are normal good links then by all means, let us take those into account.
So there you have it. Don’t be afraid to remove a massive amount of backlinks from your disavow file as that would be nothing suspicious to Google. However, be careful because if you remove links that are actually hurting your website, you are in for a lot of trouble.