You can't change the atmosphere of a gas giant to "none" via an atmosphere converter because there are no planets of that type in SectType.txt, and you can't add any like that via editing the file, either. The program is program is apparently hard-coded not to accept a planet type like that. Here is a quote from the notes in SectType.txt:
"NOTE: The following combinations of plant physical type and atmosphere are not allowed: Gas Giant x None."
The typo of "plant" instead of "planet" is in the file, too
