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What do you mean “out of sync”, out of sync with CVS or your application server? If you are asking about CVS, you need to remove the dirs then Commit the remove back to the repository.
Try refreshing the directory itself or the parent directory. That should bring it back in sync with the Filesystem and then should be able to delete it.
To refresh, right click the item you want to refresh and choose refresh from the context menu. Or press F5 (Standard keybindings)