Just start a different war before peacing out with Savoy. The emperor can only demand unlawful territory while both him and you are at peace. Or engineer situations where your actual target is a junior partner in the war so you can take their province in a seperate peace and keep the rest of the war going while you core it.
This advice was golden. After vassalizing Venice and diplo annexing Milan, I DOWed Savoy using the revolutionary war CB. My ally France joined, which was key as you'll see for other reasons, as did Savoy's allies, including the Papal State. While still at war, I DOWed Genoa with the subjugation CB - which had France as an ally along with the Papal States and Avignon. Since the former was my ally in an ongoing war, and the latter two opponents, Genoa was alone. Not having to fight France was kind of a big deal.
Then peaced out Savoy (waiting a couple months to avoid possible CtA), taking Cueno and coring it, reducing Savoy to 3 provinces for a (hopefully) later subjugation CB. Then waited for Cueno to core and then vassalizing Genoa.
So it's January 1506, I have 14 provinces in Tuscany proper as well as 6 vassals with 20 provinces. Unfortunately 2 over the diplo limit - I need to annex some vassals, but can only do so slowly for a variety of reasons, including not wanting to trash my Republican tradition too badly. Ferrara is next to diplo annex, though. May need to take a few years to consolidate my gains.
Probably time to think about taking on Austria. (They left our alliance but offered another one which I accepted, so for the moment I am again allied with France AND Austria. The two of them fought a war against each other while I was at war with Genoa; neither called me in.) Also interesting, while I was at war Naples broke free from Aragon. Sadly before I noticed they had allied with Austria. (If I had noticed in time I would have just gone ahead and DoWed - would not have even had to take a stability hit as I have the Revolutionary War CB.). But Naples looks like one of my next targets for sure.
Edit - the clear next move is to get a subjugation CB against Savoy, call in Austria, then DoW Naples. Might even then white peace out Savoy - as much as I want to vassalize them, I probably need to wait until I absorb a couple vassals - but just use that war as a mechanism to keep Austria from coming to Naples' aid.
Second edit - even better, I can do this now - DoW Provance (Revolutionary War). They have no meaningful allies. Call in Austria, then DoW Naples. Only question will be how many provinces to take from Naples in the first war.
I'm actually thinking this would have made a decent AAR. Haven't been taking screen shots, though.