It's trying to tell you something else - The update is referring to an update within Webmaster tools its self, on how it now reports on indexed files. If you click the 'Learn More' it says:
Only data for your specific site
We do not show aggregate data for all versions of your site. While Google crawls and indexes content from
your site regardless of whether you have verified the site in
Webmaster Tools, the number of indexed URLs reported in Index status
are specific to those associated with your site version.
For example, suppose you have a site with 10 URLs that people can view
without signing in, and 100 URLs that people can only see once they
sign into your site. If you have added only one version of your site
to Webmaster Tools (e.g. http://www.example.com), you would see Index
status totals only for the non-secure portion of your site, which
would be a much lower number than for all URLs on your site.
Therefore, in order to see the index count for your secure site, you
will need to add it to Webmaster Tools (e.g. https://www.example.com)
and then select it from the Site Selector.
Similarly, you can verify a subdirectory of your site with Webmaster
Tools, and only data for that subdirectory will be shown in its Index
status (www.example.com/blog/). However, the top-level domain will
continue to reflect the total count of URLs indexed for that domain.
We do not show aggregate data for all
So if you had subdomains or https versions of your site they all used to be reported under the same site in t Webmaster Tools account, however they wont be any more and you need too add them as separate sites.