I've seen a few cases like this, where, aside from anemic links, the reason was not apparent. Nobody could figure out why the site suddenly lost their trafic. I saw another case where, aside from bad site architecture, the reason was not absolutely 100% not apparent, I can vouch for it. Super difficult to put a finger on why the site lost their traffic. :)
Ok, not making light of your situation, but making the point that a loss of traffic that is not apparent can suddenly become apparent.