For a junior member, you're only negotiating with that member. When the negotiation is successful, that member will leave the war, but the rest of the war will continue. It should check on the peace negotiation screen: if it says they're negotiating just for themselves, then the rest of the war will continue.
I've got a question of my own: In my current Poland game, i've joined the HRE and am about to revoke the privilegia. The only country not yet willing to sign up for it is Austria, who is also the big price ( the inheritance fired, and they annexed quite a bit in the HRE). Sofar i've got them up to +200 relations, but to no avail. They're still threatened by me, and don't want to sign the reform.
Is there any other way to get them to sign? Does increasing relations help even more, or will that be pointless? Will it require me to launch another war at them (i just finished one, forcing them to release several princes to get the IA i needed), or can it be done peacefully? I really don't want to revoke without them in it.