The rune goes away. It may help to think of it like this. You do lose the equipment, it gets destroyed, and the rune on it goes away as well. However, you don't lose the spell. It remains in your mind to be cast again.
In more mechanical terms, the equipment does indeed get destroyed before the card is put back into your spell book, and when you cast it again it is a brand new casting creating a brand new copy of the equipment. It doesn't retain anything from the previous casting.