its not somethign forgin to final fantasy and i think it could be used. Dissidia final fantasy allowed the player to lower there own level from 100 to 1.

as for story the only way i can see that one is to buy a item or have a out of the way (to avoid people from accidentally doing this) to reset the flags on the system, if that is possible. i imagen some flags in the system are hard coded into some items. and they are easier to mark done then mark undone.