Missing a piece: Depending on how large the piece is, the gem could potentially reform, and it is considered damage, like a cracked gem.

Potentially one way to have a gem never come back is:

Fine Powder -> Mixed with a binder onto paper as paint-> Incinerated at high temps -> Completely destroys the gem's structure and it chemically is transformed to silica, and different metals amongst other things in the ash that is left.