aakk9999 - 1:19 am on Sep 19, 2013 (gmt 0)
One night our site went down because our host said their server failed (didn't crash, just somehow failed due to a mechanical issue). When it was fixed and the site went back up, I realized that our traffic was nonexistent.
How long was the site unavailable? From what I am reading, you had a problem with a server which went down, you got the server back up and your rankings disappeared?
As jimbeetle said, it would be useful to have the exact date when your traffic has disappeared as well as the date(s) the server was down prior to traffic failing.
It would be very coincidental (although not impossible) that you got hit by the update right the day the server failed. I somehow think you need to check you do not have technical issues first.
With regards to co.uk domain, the articles that you are putting on there - are they duplicated of articles on the .com domain or perhaps re-hashed articles from .com domain or are they newly written and unique? The links to .com domain from the .co.uk domain, are they nofollow? What kind of anchor do these links have?
Note that if you have .com domain that is geo-targeted to UK and .co.uk domain, these two domains will compete with each other. There is a remote possibility that Google just decided to filter one out.
Now if I try to visit a link such as mydomain.com/product-id=4939, it forwards me to the homepage but mydomain.com/product-id=4939 is still in the address bar.
This would happen if you are returining HTTP 404 (Not Found) and sending home page HTML alongside the response. Have you checked what HTTP response you get for these old URLs?