Probably not, but...hiding system folders in tree only?

I have a button which toggles whether hidden and/or system files should be shown in a lister. Usually I have them hidden, to reduce clutter, but occasionally I need them visible and accessible. However, whether my button is on or off, hidden and system folders always show up in the folder tree. I'd rather they didn't when I have my button off. I can't use the option to "hide protected operating system files" because then my button that allows me to see them when I need them doesn't work. Is there any way around this?