I love Flash Builder—especially the refactoring help—so it broke my heart when I found that many of my favorite features, such as renaming variables and classes on the fly, didn't work. I was also getting all sorts of weird other problems, such as getting two copies of warning and error messages. I also couldn't edit files when I spotted problems in debug mode, because I'd get a weird error message that the file I was trying to edit was a "generated file," whatever that means.
Finally I figured out that all these issues were symptomatic of the same issue—accepting Flash Builder's defaults when I created a new Flash Pro project. Let's take a step back and look at what the history of my project was. First, the team I am on primarily develops in AS2, and we have a lot of relative path #includes and a source path that point to the same place on everyone's hard drive. To support this, everyone has the same directory structure.
At the moment, I'm reworking the existing code into AS3, but the last thing I want to do is introduce an unfamiliar directory structure. So I used the normal team directory structure and pointed my Flash Builder project at the usual location. What I somehow failed to realize was that Flash Builder has a default place it wants projects to be, so it created a directory in that spot with the same name as my xfl file. This is where all my actionscript files were being "generated" to for use in Debug. Not only did this cause the "generated files" method, but somehow it borked most of the refactoring support in the project.
Next, I deleted the project, making sure to deselect "Do not delete contents." This gets rid of the shadow project and its files. Next, I added it again (File>New>Flash Professional Project). When I selected my target file, I unselected "Use Default location." Since this is an XFL project, when I clicked the "Browse" button next to "Project Location," I navigated to the directory that contains the directory with my XFL file in it. If you were doing this with an fla project, you'd probably want to navigate to the directory with the fla in it.
That fixed the problems with the day-to-day operation of the project, but it created a new one. My project uses xml files to drive a lot of the content, and these were no longer loading properly when I launched the project from Flash Builder, though they worked fine when launched from Flash Pro. The reason for this issue is that Flash Builder created a bin-debug folder next to my xfl folder, but we traditionally expect that Flash Pro will make the swf next to the xfl (so that is where the XML files are stored). The final step is to go into the Project Properties in the Run-Debug Settings and edit the path to point to the root of the project.