Flash still has the ASO file, which is the compiled byte code for your classes. On Windows, you can see the ASO files here:
C:\Documents and Settings\username\Local Settings\Application Data\Adobe\Flash CS4\en\Configuration\Classes\aso
On a Mac, the directory structure is similar in /Users/username/Library/Application Support/
You can remove those files by hand, or in Flash you can select Control->Delete ASO files to remove them.