The Federal Court is the ultimate appeals court and thus can overrule the Patent Court, hence forcing the German Patent Office ('Patentamt') to grant the patent.

What's more, and potentially worse, judgements of the Federal Court serve to interpret and further develop the law. Hence it is very much like a precedent in the common-law sense - except one that isn't open to interpretation by other courts. If legislators now think that this is not what they intended, they are free to change the law. But you'll find other courts very much basing future judgments on the opinions of the Federal Court.

The European Patent Office has granted a fair number of software patents for technical solutions (indeed, the issue of "technicity" is key) using software. So this may point to their validity in Germany and increase litigation.