It's pretty frustrating when you win a war against a major power that's supporting your puppet's independence (or even against the puppet itself) and the support treaty just... stays there. Laughing at you. Eventually the game gets to a point where all your rivals will go out of their way to support the independence of all your protectorates, leaving you stuck with their liberty desire maxed out. As far as I know, there is currently no way to deal with this in vanilla.
I wanted to share an underrated mod from the Workshop that fixes this issue. It's the "Revoke Supporting Independence" mod. It makes it so that enforcing a Humiliation war goal breaks any support independence treaties, and I honestly can't play without it anymore. It doesn't completely wipe all treaties the AI makes, but it does strip away the independence support article and prohibits new ones being made during the truce. Before finding this, I was getting to the point of avoiding protectorating countries I intended to annex, because the second a major power decided to back them, that +0.20 modifier would be stuck there forever.
I believe it's something the devs could just integrate into the base game (like they've done with other mods in the past).