If you don't take down something you get a DMCA notice for, do you lose safe harbor status for everything, or just for that one thing? If the latter, then wouldn't it be a good move for GitHub to ignore DMCA requests that their lawyers are sure wouldn't hold water?
As I understand, there are different safe harbors and each applies at the "service" level. It's "online service providers" that have safe harbor status.
If you lose safe harbor status you become liable for infringing content on that service.
Infringement still has to happen and you'd still have to be taken to court and lose, but it's now "as if" you yourself uploaded everything.
So in this instance GitHub would be fine, but if they didn't take down the content then they themselves would become liable for any fringing content on their platform.
Or rather Microsoft would become liable, I suppose.