First, do Freeform Combos animate in the same fashion as normal combos? As in, do they animate even when they're not being displayed?
Second, is there a way to get them put back to their starting position during a loop? An idea I have is to make it look like you're falling, having stars pass you, emenating from a certain point on the screen
I can't answer the second question (though I can question why this is in the normal ZQuest Editor Help subforum 😉), but for the first, I'm almost positive they do continue to animate. I recall hearing a method for making time work on the entire overworld by putting the same FFC, which animated/cycled, on every screen on the overworld, and then when it hit 0, no matter what screen you were in, it'd direct warp you to a new version of the overworld (night, for example) where things were changed. So, yeah. That's what leads me to believe they do constantly animate (because if they didn't, the timers would reset every time you went into a new screen).
I believe they constantly animate as long as you've set its carryover property.