I have just spent the last 2 hours trying to figure out why my none of my changes were reflected in the compiled SWF.
Thankfully I came across this post where one of the comments had the solution.
If you have a SWF named <PROJECTNAME>.swf in the html-template then deleting it will fix this issue.
Apparently the existence of this file means that when you do a Build or Release Export it just copies this file and does NOT compile the latest source code.
Makes sense to me!
It turns out that it’s a known bug which has never been fixed, but I hope it’s been fixed in Flex Builder 4.
Hope this helps someone having the same problem in the future.