So formally, the Treaty as such was never challenged.

That the challenge is of the approval law is only logical, as the Lisbon Treaty is not in force itself at the time of the challenge. However, it is possible to challenge the treaty indirectly by challenging the legality of any approval law. That is seemingly what some of the litigants did, and the Bundesverfassungsgericht rejected those challenges.

I haven't had time to read the judgment of the BVerfG, but it seems from the press reports that Karlsruhe continues to uphold its German exception, that being, their own right to annul EU laws they see as being in conflict with the German Grundgesetz. This was already one of the key elements of the judgment on the Maastricht Treaty. The Bundesverfassungsgericht has never actually done this, mind. It just preserves the right to do so.