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OmniFocus will keep an action that's been edited around for a while even if it doesn't match the current filter settings; if you edit something by accident, we want to keep it around so you can notice/correct that. The app used to whisk items away a lot more quickly and folks asked to change to the current behavior.

The next time the view in the window changes substantially, though - switching between modes or perspectives, for example - everything will be shown/hidden/moved at that point. (You can also force a Clean Up via toolbar/menu item/keyboard if you want them to do so.)

Hope that helps!