-The Totem of Undying isn't affected by /clear.

Steps to reproduce:
1) type /give @p totem
2) type /clear @p totem
OR
1) type /give @p totem
2) type /give @p cobblestone
3) type /give @p netherrack
4) type /clear @p

Either way, the totem won't be removed from your inventory. It's as if the game doesn't register it as an item.-

This probably was a ghost item, what threw me off was the error message "there is no such item as minecraft:totem".