When you use CSS Form Builder to update an existing form it will recreate the form based on the settings that you have chosen. If you would like to just add captcha to your form you might be able to make use of a technique that I have seen others post about. The idea is to create a new form with the CAPTCHA added to it then transfer this to your existing form. This would allow you to leave your forms in their default state and just add to them rather than modifying them with Form Builder.
You would just need to make sure that you transfer the captcha potion of the form including the image and input then also add in the validation code. If the only think in the form that you create is the captcha it would be easier to work with.