Brief history:
I am MD of a medium sized health organisation in the UK. We have one of the leading websites in the world for our industry. We were hit by a Google algorithm update last year (Penguin or Panda, I can't remember, but that's not relevant here I don't think) and our daily visits went down from around 10,000 to around 5,000 in two separate hits over a couple of months. Then there was a steady decrease to about 3,000-4,000 visits a day until we totally updated the design of the site and did some good work on the content. We have always been white-hat and the site has around 3,000 pages with unique content added daily.
So things have really been on the up for the past couple of months. We have been receiving around 6,000 visits a day in recent weeks (a slow incline over the past few months), until Sunday. Sunday morning around 10am all of our organic listings pretty much disappear, including for our brand name. Monday morning a few come back, including our brand name and our main, most competitive keyword, which we were showing up on the third page for and we returned to this page. Then Tuesday morning another few of our most competitive keywords show up, back where they were before. This includes images which had disappeared from Google images.
Our PPC and business listings were not really affected at all.
My developer submitted a site map through webmaster tools on Monday morning and I'm not sure if this is the reason pages started to show up again. In our Webmaster tools the indexed pages are about a quarter of all of the ones on the site - all pages were indexed before. I just don't know what has happened! It doesn't make any sense as 1. Google don't seem to have rolled out any algorithm updates on that day 2. we do not have any messages in Webmaster Tools 3. a number of our main keywords have re-appeared - why would that happen if we had been hit by a Google update?!
Our organic hits, which previously made up about 80% of all our hits, have gone down by 80% and this is drastically affecting business. If this continues it is likely we will have to downsize the business and I'm not sure what to do.
When I saw that the 'indexed pages' in Webmaster tools started to increase (they were around 600 on Monday, around 900 yesterday and then this morning, around 1,300), I thought that we were on our way up and maybe this problem would just resolve itself and our listings would re-appear, but now our indexed pages have reduced slightly since this morning, back down to around 1,100 so the increase has stalled.
Can anybody help?! Do you have any idea what could be causing this? Apparently there have been no changes made to robots.txt and my developer says that no changes were made that could have affected our listings.
ANY ADVICE WOULD BE GREATLY APPRECIATED.