Are bonus jewels discarded after use?
You turn the card over after using it.

While this isn't explicitly covered in the main rules, there's an example of play at the end of the rules that clarifies the issue. In the example, Gollum and Orcs are used for bonus gems, and then turned over.

The German rules can be found here, and have the example "Beispeil" on page 7. It ends with:


  „Gollum“ und „Orks“ werden umgedreht. ("Gollum" and "Orks" are turned around.")


This is also in the unofficial English rules translation.