I recently found a bunch of old files that had been ftp'ed to a live production server by mistake on a static (html / css / js) site. I manually deleted these files, but today when checking in Google Webmaster tools i found this graph below. The 'update' marker is from 3/9/14, what i can work out is what Google is trying to tell me, are they saying that :There was a ranking update like Penguin or Panda and they penalized my site and un-indexed a load of pages which they thought were junk.. OR Is this showing that I updated the site by deleting the files on the server on 3/9/14OR Is this something else ?
Reading 'Index Status' graph in Google Webmaster tools
google search console;google index
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 allSo 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.