Hmmm... I cannot seem to re-create the issue in my test environment. I have a passive state checking the enemy HP and if below a certain amount the <Custom Initiate Effect> adds the charge up state with the <Custom Apply Effect> that adds stacks. The charge up state and all stacks are removed when they are hit. The filter is removed with it. It comes back if conditions are met and removed the same. It's a dumbed down version of what you are doing but shouldn't matter much since the main user.addState(x) calls are there. I suppose I could maybe add a call to remove all filters from a battler you could use if we can't figure it out?