I don't know your detailed scenario, but for now, please just overwrite/add the entry using the latest version of the script. I'm sure it's no problem having the desired entry(and value) set in your build.prop in any case. However, if somehow you encounter problems with adding an prior non-existent entry, feel free to report it here and I'll push another release supporting your rare case of editing lines.
It would be beneficial to change a value if it exists but do not add it if it does not exist. Some entries can contradict each other so if one value exists that would cause an issue with another, it would be great to not add both entries with different values.