I have a good feeling about this, and I never really believed the deal would stay dead once Lynch and Frost's scripts were done (which they allegedly have been for a few months). It's easy to kill a project early on, but Twin Peaks is a valuable property and too much is at stake to relegate it to development hell at this late stage.
Showtime dropped the ball when they announced the production last Autumn without an agreed-upon budget firmly in place, and they pretty much handed David Lynch the Artist vs. Suits trump card on a silver platter, exactly the kind of the situation Showtime - in their effort to be both premium and creator-friendly, post-Dexter - should have taken great precautions to avoid. If Showtime wants to stay relevant, they can't afford to lose this. Frost and Lynch, on the other hand, can.
I'm pretty sure Lynch used this very well to his advantage (although we don't know the details), and squeezed a better shooting budget out of the deal. Although, looking over the statements, it's also tempting to speculate that the issue may have been a question of running times. Maybe Lynch and Frost's final scripts turned out to be too long, and that a new deal had to be struck to account for extra (and/or longer) episodes? It seems reasonable to me, especially if it is meant to be a conclusion to the series. Writing conclusions is notoriously difficult, and Lost's final season became almost two episodes longer than it was supposed to be.
Anyway, I'm really happy about this!