Right-click on your project, go under the Index submenu, and choose either "Rebuild," "Update with modified files," or "Freshen all files."
I don't know the difference between those three options, but one of "Update with modified files" or "Freshen all files" usually fixes it for me.
Also, I'm sure you've already done this, but make sure that you're running the latest version of the Eclipse CDT. Current versions seem to have much more reliable indexing than previous versions.
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