What was used instead of the failed engine when ferrying the Air France Flight 66 aircraft back?
Here's another article from Oct 15th. They flew out a spare A380 engine. As of the 15th, it wasn't clear yet if this engine will be connected and running during the flight, or if it'll just be there to complete the airframe and act as a counterweight. 

Leaving the broken engine in place would do more damage to the engine, complicating the investigation. 

Pieces breaking off from the engine may have damaged the wing, the pylon or the connectors on the pylon (power, fuel, electronics etc.), they need to inspect for damage before deciding if the spare engine can be connected and running. 

The plane will be empty for the recovery flight, so there's some margin to fly on 3 engines. They have to account for the possibility of an engine failure, leaving 2 operational engines, so the flight is planned to ETOPS rules. 
There's a procedure to reduce the effects of asymmetric thrust. 

If the engine is left off and windmilling, it needs lubrication, this may limit the length of the flight.