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.