tedster - 10:28 pm on Feb 12, 2013 (gmt 0)
I have 18 links left and none to any index page
That's the clear signature of this issue - the loss of link reports for index pages. Those can't ALL be untrusted links. I think they are initially compiled separately from internal links and the two are then combined in a later step that went haywire.
This is a kind of process that Google uses for URLs in the actual SERPs that has gone buggy in the past, resulting in the loss of any traffic to some index pages! Luckily, this current loss seems to be just in the reports and not in the actual SERPs.