You can insert cue-points live from the client with netstream.send, and from the server into a live stream with this method:
http://community.wowza.com/t/-/238#2
I made something awhile back that involved a flv converted from PPT with Captivate, and a live stream where the speaker could flip the pages using netstream.send. It was a little involved, and required output of Captivate, but to my point that there are a lot of possible scenarios. A lot synchronization efforts have come up short. Many have tried with little or no success to replay a live chat, for example.
Richard