Cleaning Up
The grouping, sorting, and filtering settings in the view bar control what parts of your database are visible and how they're arranged. For instance, most of the time you don't care to see actions you've already completed, so you use the action filter to show only remaining actions. Sure, that's handy, but you also don't want OmniFocus pulling stuff out from under you as you're working on it. For instance, if you mark an action complete, you probably don't want it to disappear that very moment; you may still change your mind and want to uncheck it, or copy its notes into an e-mail, or just double-check that you clicked the right thing. Likewise, you probably don't want an inbox item to be spirited away the instant you assign a context to it.
So, OmniFocus has a command called Clean Up. It happens automatically every now and then, so that things stay tidy, but you can also clean up manually by clicking the Clean Up toolbar button, or choosing Clean Up from the Edit menu.
Cleaning up puts everything where it belongs: items that don't match the filter settings disappear, visible items move into the appropriate groups, inbox items move to their assigned projects, and so on. After you change some items, you can Clean Up to make sure that your view is up to date.