The problem is that, if one of the parts is the root of the entire craft (the part you started with), you can't just take it out. There is a way to do this though: Detach the REST of the rocket from your main pod. Now delete the pod. You can now do nothing with the rest of the rocket (which is red, the same way a part you didn't attach would be) until you pick a new root part. Pick for this the other pod. Now reattach the rest of the rocket to this new pod