I think the main points about replacing both engines is..
It does not take twice as long to replace two engines as it does one engine, so the airplane can be back in service sooner.
If there is any performance improvement package available then a matched pair is obviously the way to go.
An engine does not loose its value by being taken off the plane, it is still worth exactly the same in the engineering bay as it is on the pylon.
A spare engine is an asset to the airline, it is an additional economic utility.