Google Webmaster Tools indicates "Links to Your Site" Dropped 91% after some site changes

Question

Today I noticed that "Links To Your Site" in Google Webmaster Tools dropped from 2130 to 23, and from 122 domains to 11 domains. That's more than a 90% decrease!!

After some researching, I noticed that something similar happened in 2013 and it was due to a Google Technical problem. But that was 2 years ago and I haven't found any recent articles. What could have happened?

It's impossible that all the sites deleted links to my domain, because I own some of them and the links are still there, while they are not listed anymore in Webmaster Tools.

I recently made these modifications to my website:

1. Moved all the source code to CodeIgniter (tested and working with just some minor bugs to fix)

2. Optimized the website for mobile using Foundation

3. Introduced HTTPS and forced it to all my URLS

4. Changed all <link rel="canonical"> from HTTP to HTTPS

Could one of these have been the cause of such behaviour? (Even if it doesn't look logical, because I made no changes on the domain). If not, what could have happened?

Answer 1

Providing that only the protocol changed for your URLs, it's most likely number: 3. Introduced HTTPS and forced it to all my URLS

When you change the protocol (e.g., HTTP -> HTTPS), the URL changes, and links from other sites will still have the HTTP version of your URLs.

If you're properly redirecting HTTP to HTTPS using a 301 redirect, then it will take some time for Google to recrawl backlinks to your site and be redirected to the new HTTPS version of the URLs.

As indicated here by Google, be sure to test that all HTTP links are properly redirected and reachable under HTTPS.

You'll also want to make sure your robots.txt reflects these changes so it's not inadvertently disallowing any HTTPS URLs, as indicated here.

As covered here by Google, you should try to update incoming links wherever possible, such as:

• External links: Try to contact the sites in the saved list of sites linking to your current content, asking them to update their links to your new site.
• Profile links such as from Google+, Facebook, Twitter, and LinkedIn.
• Ad campaigns to point to the new landing pages.

For internal links, you'll want to make sure you update links within your site (e.g., navigational links) to reflect these URL changes. Also be sure to update your sitemap to reflect them as well.

(Note that you do not need to submit a Change of Address in Google Webmaster Tools for protocol changes.)

Last but not least, it's wise to make sure you're not mixing content in your pages (e.g., all links on the page are either HTTPS or relative), so that visitors will not be getting SSL security errors.