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Can you tell from when did this problem start? Are you using an old Flash Builder workspace?
You can perform the following steps to resolve the problem -
1. Clear the cache - to clear the cache,
a. Close Flash Builder
b. In Explorer/Finder, go to folder -
If the above folder does not exist, then see whether [your workspace]/.metadata/.plugins/com.adobe.flexide.codemodel.bridge folder exists
c. delete the searchCache, SwcCache and swcCommentCache directories
d. Open Flash Builder. It will re-generate the caches and things would work.
e. If things do not work after this step, then follow step 2.
2. Create a new workspace and import your projects in that workspace.
The steps for cleaning the cache didn't work. Unfortunately, FB won't allow me to import the project. It claims the directory it does not contain a valid FB project. Could it be because this is a Flash Pro, not Flex, project? IOW, the Class files are supporting an xfl folder, not MXML.
BTW, I'm not sure when it started. I was off doing Flash/AS2 work for a month, and it seems that when I came back, this stuff was broken. But it might have been working for the first day or so--it's so much more noticeable when something isn't working than when it is.
I eventually discovered the problem--Flash Builder was creating the project in a totally different directory from where my XFL and source code were http://flexdiary.blogspot.com/2012/07/when-good-flash-builderflash-pro.html
Thank you Sameer, that solution worked for me.