Hmm. The Swabian war comes at an interesting time for the Confederacy. Her military expansion had accelerated, netting her more allies and a major victory over the Burgundians in 1475, but the Habsburgs remained a strong influence in the Three Leagues and the Rheintal until this point. I'd say that it depends heavily on how bad a defeat it is. A serious one will see Austria incorporating the Toggenberg inheritance in the League of the 10 Juridstictions and her presence the Lower Engardine much more, possibly including effective puppetisation of what's left of the Three Leagues under the Bishop of Chur, and she'll definately be aiming to push more into the Rheintal after this. A minor defeat is likely to be, effectively, status quo ante bellum given that the Habsburgs were fighting very defensively.
Either way, I forcast further conflict in the near future.