I just ran a test and was not able to reproduce this.
I have found with Dreamweaver that if you use the File Inspector along the top to open a linked file like the CSS, that file wont get updated unless you close Dreamweaver.
It doesn't seam to have this issue if you open the file directly from the file panel.
one way you can prevent Form builder from overwriting changes is to create a second css file and add the link to it after the link to the form builder css. use this second file to over ride form builder css settings.