Deleted Folders Stay Visible

This seemed to start just recently, but when I delete a folder from a project (using right-click, delete from within CFB), the folde stays visible with the red X.
How do I get these to go away?
RLS

Yes, I am using a source control.
I have committed numerous times, rebooted once, restarted ColdFusion Builder twice more on top of that. They just won't go away. Quite frustrating.

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