It might be nice to retain the options using GM_setValue/GM_getValue.
Hm. I liked leaving them all on to start with, as doing otherwise requires processing the page without user input.
But a manual way to save the filter options (and the current number of notes displayed), available via the User Script Commands menu -- that I'd be happy with adding. If you code it up, I'll gladly add it -- or I'll get around to it eventually.
Yes, please, at least just remember selected checkboxes for next time, it requires user's work each time I want to filter stuff when I could just click one button if it was remembered...