Flash CS4 refuses to let go
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.
Try deleting your ASO files.
ASO files are cached compiled versions of your class files. Although the IDE is a lot better at letting go of old caches when changes are made, sometimes you have to manually delete them. To delete ASO files: Control>Delete ASO Files.
This is also the cause of the "I-am-not-seeing-my-changes-so-let-me-add-a-trace-now-everything-works" bug that was introduced in CS3.