If I understand you correctly, you have your user presets showing up twice in H9 Control.  Would you want to just delete all of your user presets and start over?

On Mac all of the user presets are stored under your user's home directory at Library/H9 Control/Presets.   

On Windows all of the user presets are stored under your user's home directory at AppData/Roaming/H9 Control/Presets.

You could just delete this Presets directory.