EDIT: Josh mentions the Font.registerFont already.
When you say separate projects, do you mean 'projects' in the IDE sense? Are you using FlashBuilder (or another IDE?) setting the font/asset project as a dependent project? And using Link type: merged into code?
Not sure how your ttfs are embedded, but I actually also use a separate FB font project as well, and made an ant build script to use the command line fontswf tool to turn the ttfs into individual font .swfs ahead of time and embed like:
public static var MyFont:Class;
and then also make sure I call on startup (which I am not sure is required but safe):
I think embedding the original .ttfs instead of .swfs should work the same way though (but I think making the font .swfs ahead of time (since they won't change often) improves compile time as the .ttf isn't converted to the swf code each compile??)