This is an issue I've battled more than once while developing a flex project with flashbuilder. This is most commonly caused by the flex sdk copying source files into the html-template folder. When this happens, the precompiled sources are used from the templates folder instead of being recompiled when the project is rebuilt. To solve this problem, you can either remove any source files you want rebuilt from the html-template folder under the root project directory or just deleting the html-template folder itself (flashbuilder will automatically recreate it on the next build).
I've wasted many hours on this problem in the past. Hope this saves someone some time.
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