JD_Toims - 4:41 am on Sep 19, 2013 (gmt 0)
Based on personal experience [I had a site not get auto renewed and make it to the redemption period before I noticed (28+ days) but it came back within a week of renewing it.] I would say the "downtime" was not the issue, because even if the site didn't show in the results for a week or two due to downtime it should have been back not too long after it was back up.
As far as Anlytics go when I run an "overview" from July 9th to July 12th, I see on the 9th we had 879 visitors, the 10th 716 , the 11th 409, and the 12th 372.
This is also not an "Oh, our server went down" drop pattern -- If a site's server goes down and it gets dropped then re-indexed the visitor pattern should go the other way. Meaning it should go from 0 and continue up, not slowly drop.
That being said, the SEO company that we have hired - to be completely honest - has never sent us any reports as to what they have done (a list of lists of sites they posted to, a list of backlinks they created, etc) over the years. I've always asked for reports and they were promised, but they remain very secretive about exactly what they do. Maybe they were secretly submitting blackhat SEO (possibly?) but I really believe that most companies won't give away the secrets to their trade.
-- Best guess after skimming through the long messages in this thread: the preceding bit you in the A** with Penguin 2.0 and any type of duplication [to be non-duplicate 85% or so unique is the last % I remember hearing] on the .co.uk domain probably didn't help, because duplicate content is duplicate content and I'm not sure who said it wasn't considered a duplicate on a separate domain, but they're incorrect.