[whpalmer4]

There's an Edit->Clear Flag command available when you have selected something that is flagged. Select all of your flagged actions and use that command. Easiest probably to do this in context mode, like the built-in Flagged perspective does, but there's a wrinkle -- if you've flagged a project, all of its actions are treated as if they are flagged, but you won't be able to clear them from context mode, only by clearing the project's flag, which you do in project mode.