I was worried about this too, but for testing crafts such as planes and rockets, I've been using the "Revert to Spaceplane Hangar" or "Revert to Vehicle Assembly" options in the end-flight dialogue. I have found this to be way better than the previous system, because it reverts the game timer as well as the flight, so it acts as if the test flight never happened in your persistence file. However, for longer test missions (such as interplanetary tests), I created a new save file labelled "test."