Why doesn't GE replace all 4 engines for on their flying test bed instead of just 1?
They only change one, because that one is a new engine that is being tested.

If you are testing a new engine you change 1 at first so if it fails you have 3 others.  If you change all 4 and there is a systematic defect in the design, now you have 0 good engines instead of 3.  



You will also see that the test engine isn't always one suitable for a 747.  This is because they may be testing a new design or a new alternative fuel and it is safer to test an unknown with 3 good engines (e.g. a 747) rather than with just 1 good engine (any two-engine airplane).  This increases the safety margin if the test engine fails.



Running a different engine with a different thrust rating requires some thought about asymmetric thrust.  Doing this on a 4-engine airplane simplifies this greatly over a 2-engine airplane.  Ways to accommodate different thrust from the odd engine:


De-rate the new engine so it only produces thrust equivalent to the normal engine
Run the new engine at reduced thrust
If the new engine is inboard, reduce the outboard engine thrust to balance the total yawing moment from that wing with the other side.
Don't worry about it and trim the airplane to compensate.


The other advantage to doing this on a 747 is that a 4th engine is technically not really needed as a 747 can takeoff, fly and land with only 3 operating engines.