In moving to compiling projects with the new Flex SDK 4, in noticed a couple of gotchas to do with the EMBED metatag that I thought I'd better share:
Runtime shared libraries
If you're like me and want to embed assets in your project with the EMBED Flex metatag, so you can manage and update things easily, there's a an extra compiler parameter you must add, in order for your project to compile properly:
--static-link-runtime-shared-libraries=true
This is already added as a new default parameter to the new version of FlashDevelop. But if you're planning to build projects from outside of FlashDevelop, you must add this to your compiler string. Otherwise, the compiler will think you have uninitialised constants and warn you so.
Embedding fonts
Using the EMBED metatag (or runtime loading) for fonts is the sensible way forward. The amount of projects I've seen where you need to build from an FLA file full of fonts you need to install that you can't find is crazy. With Flex SDK 4, you'll need to add an extra attribute to your embed tag for fonts, called 'embedAsCFF':
public static const MY_FONT :Class;