The infrastructure update Google Search Console could temporarily affect the data in the report "Links to your site". About this said the representative of the search John Mueller in response to a question from webmasters.
Last week, some site owners have noticed a significant decrease in the number of links in the report. One of the resources downturn was 50%.
In response to the question about the possible causes of these changes, John Mueller reported that the decline can be associated with data refresh from Google. According to him, to worry about it not worth it.
@pedro_matias @methode Disavow doesn't affect which links are shown. That sounds more like data-changes on our side, I'd ignore it.— John Mueller (@JohnMu) 30 Dec 2016
Google currently holds the infrastructure update Search Console that may have a temporary effect on the performance reports.
