Who told you that a change in the parenting plan would reset the clock?
I don't have any idea how the process works in your state, but I would suggest that you ask an attorney.
As for 'protect my children', there are two issues. First, if they're his children, as well, you need to stop with the 'my' children stuff immediately. You can't just ignore the fact that he's their father and if you try, you'll get slammed in court. Children do best with regular contact with BOTH parents.
Now, if the children are truly in danger, that should be your priority-it is far more important than whether you get your divorce today or a few weeks later. If there's danger, contact Child Protective Services. Then, ask the court for custody and/or a protection order - whichever is appropriate given the circumstances. If it is truly an issue of danger, you can get a protection order without changing the parenting plan. Unfortunately, there's no enough detail in your post to offer any specific suggestions in this area.