As you know, enemies with the 'Is Invincible' Flag checked are invulnerable to all attacks, but most of them can still be stunned by the fire boomerang (those that are invulnerable to Wooden Boomerangs would not be affected by the fire boomerang).
However, invincible enemies are not affected by the Kill All Enemies Item or the death of the ring leader (Except Ghinis), but they still prevent shutters from opening, Push (Wait) Combos from being moved, and secrets revealed by killing all enemies from being revealed (except Bubbles, Zoras, and any type of enemy that would be invincible regardless of the flag).
And putting such enemies in areas that you have to pass through in order to make progress in your quests could potentially make it impossible to get through those areas without using the No Walls Cheat if at least one is at the top of the list of the enemies on that screen.
Perhaps it would be a good idea to implement at least a couple more enemy editor flags:
1. 'Is not affected by Ring Leader/Kill All Enemies' (Those with the flag un-checked would be affected by such)
2. 'Does not affect Shutters/Push Blocks/Secrets' (by which I mean, they would not prevent shutters from being opened, push blocks from being moved, or secrets triggered by killing all enemies from appearing)
