One thing I failed to mention is that when I create the custom style sheet, I copy/paste the same selectors that Form Builder creates into my custom stylesheet. And keeping that stylesheet below the one that Form builder creates in the cascade is key. When working this way you don't necessarily end up with an old and new stylesheet, but more so a modified version of the original that was created by Form Builder. If you re-enter the editor, and make any changes to your form, the custom stylesheet should still apply because its referencing the same classes and IDs that Form Builder applies. Changing those classes and/or IDs outside of Form Builder will obviously require changing your stylesheet selectors by hand so that they match.
Are you changing html structure outside of Form Builder? Are you using classes and IDs referenced in your stylesheet(s)?
Also, there have been a few threads on her where Jason or Ray have stated that Form Builder is more so a one-time form creator than a form editor. But I've been able to leverage my process to go in and out of the editor with ease without losing customization outside of Form Builder.
I do remember documentation stating that you can covert an existing form into a Form Builder form, then edit it from there. Personally, I haven't done one this way. I imagine that once you convert your form to a FB form, FB will apply its own stylesheet and you need to use that. Then you can append a custom stylesheet like I mention above.
Let me know if I'm still not understanding you correctly.