Update: Turns out I was incorrect about the relationship between the old patent and the new one. The ruling may (or may not) have some influence on the suit over the new patent, but it is not determinative.
This is getting very complicated. I'll try to get a post up about at least some of the many permutations of possible outcomes soon.
Today, the U.S. Patent and Trademark Office posted its Action Closing Prosecution (nonfinal). We're still studying the lengthy document, but all 57 claims of Blackboard's 6,988,138 patent have been rejected - the original 44, plus the ones they attempted to add during the re-examination process.
Here's the PTO document about Actions Closing Prosecution.
The USPTO has now ruled against the patent twice. They made a preliminary judgment of invalidity, they gave Blackboard a chance to rebut that judgment, and then they said again with today's announcement that they still think the patent is invalid. Blackboard now has 30 days to make one final attempt at rebuttal. After that, Desire2Learn has 30 days to respond to Blackboard's response, at which point the USPTO will issue a final judgment. Assuming that the third judgment goes the same way as the first two, then the patent will be officially, legally invalidated. Blackboard would be able to file for an appeal in the courts, but they would be fighting the USPTO, not Desire2Learn.
But there may be even more here. If I understand this announcement correctly, this invalidation applies not only to the original patent but also to the continuation patent that Blackboard was recently issued and over which they have initiated a new lawsuit against Desire2Learn. (I'm seeking confirmation on this point and will update this post when I find out more; it's a bit hard for me to parse since I'm legally constrained from looking at the documents directly.) If so, then this ruling is very significant indeed. It could be the beginning of the end for this whole chapter in the history of educational technology---after Blackboard spent many millions of shareholder dollars pursuing the litigation while failing to put Desire2Learn out of business, failing to prevent Desire2Learn from acquiring new customers and developing new versions of their products, and creating a popular backlash that could have a lasting effect on the Blackboard brand. (The Facebook Million$Mission group has 347 members after just a couple of weeks of existence and appears to be growing daily.)
At this point, Blackboard might be wise to take up Desire2Learn on their Million$Mission quickly before D2L takes it off the table. It may be their last opportunity to extract money out of their rival and save some face in what appears to be turning into a financial fiasco for the company.