I am part way through a project using a particular font. When I opened the project today AE is says the font is missing. When I open Font Book I can see it there, but AE doesn't want to load it for some reason. It loaded it last week, but not today. I am using CS5.5 on a mac with 10.6.7.
Another thing you could try is to see if you can find an alternate version of the font online. Like if it's a .otf file then maybe try a .ttf version if one exists. Or convert it with a font conversion utility.