Probably not... the flexing chainstays on the scalpel wouldn't perform properly if they were extended to fit the larger wheel. My vote is to do a 29er Rize and drop the travel down to 100mm. The faux bar suspension performs better anyway...
The comfort and cush of the 29er wheels combined with the S.A.V.E. built-in vertical flex of the new Flash would, I think, make a race 29er FS pointless. My opinion, maybe Cannondale's too but there wont be a 29er Scalpel for 2010. Word on the stree... word on the trails is 2011 will see a refreshed Scalpel... maybe then? Again, IMO, a 29er Flash is a better idea, lighter, less trouble and maintenance, as much comfort and cheaper than a 29er Scalpel would be...
Judging by the comments here, 29er bike performance is a new dynamic for Cannondale and its riders, and that's fine.
Flexible chainstays would work fine for a 29er; just reduce the travel to 3". It is standard fare in the 29er world that 3" 29ers give equal squish as 4 or 5" travel 26ers. There are several good bikes with this spec being sold, but the opportunity Cannondale has is to make one that's both tough and super-light, something that other companies have struggled with a bit.
Hardtails with carbon seatstays don't make softtails pointless, the Salsa Mamasita is an example of a production bike like this and it would certainly give more sting and bounce down a bumpy descent. There are two 1" 29er softtails on the market with metal chainstays that have been selling for quite a few years and a newer 1.5" softtail.
Since that's circa 2007, I'm going to gather based on other rumors I've heard that Cannondale prototyped a bike like this and never brought it to market.
Look, the flexible carbon seatstay/chainstay is a proven Good Idea. 29ers for the highest level of enduro racing: Good Idea. Maybe that Aussie in the "24 Solo" documentary wouldn't have nearly killed himself winning against Eatough if he was on a 29er Scalpel