If an asset isn't used on stage (for instance, popups that you add to the program with getDefinitionByName/addChild), it seems that the AuthorTimeSharedAssets doesn't always update properly. Is there a way to manually update the link?
FWIW, if you go into the Symbol properties and uncheck "update automatically," then go back to the library and check the "link" box, this usually forces an update (and even allows you to say whether the shared or local symbol takes precedence).
It also seems my issue wasn't that the assets weren't used on stage, it was that each xfl has its own subfolder (which is a bow to how FB expects you to structure a workspace when you're pointing to a Flash project).
In Flash CC, Authortime Sharing of library assets has been removed and only Runtime Sharing is supported.
If you are using CS 6, then you may right click on your shared symbol in the Library panel, select the Update option and manually do an update.
Yes, the above "CS 5.5 only" section is applicable to CS 6 as well but not in Flash CC.
The new update(Flash Pro CC release - November 2013) is now available to you; which has the Authortime sharing feature enabled. This Flash CC update will update your flash version to 188.8.131.52.
You can update from the Adobe Creative Cloud application or from Flash Pro CC Help -> Updates menu.
You will more information about the update at: http://helpx.adobe.com/flash/using/whats-new.html
Adobe Flash Professional Team