Hey, no something's off there. After you save a factory preset with a new name, it's no longer a factory preset, and you should be able to overwrite it. The new preset should appear with a U prepended to the name to indicate that it's a User preset. And any changes to that U preset should cause H9 Control to ask you whether you want to overwrite the existing user preset or create a new one.
What platform are you using H9 Control on: iPhone, iPad, Mac OS X, or Windows? And which version of H9 Control do you have? You can figure that out by clicking on Settings on the bottom right hand corner of H9 Control and going to About. The latest version of H9 Control is v1.3.2.