Flashpoints show up in career mode or after the campaign is completely done. They do not replace travel missions.
I've still only done a few myself, but they show up even if you're on the other side of the map and you get some basic information about them. You can head over to the relevant planet to take them or just ignore them and let them expire. They can be configured with time passing between missions and/or immediate consecutive missions.
Come to think of it, it's probably technically feasible to add deployments back in as the replacement to travel missions that they were before... I assume they aren't working because some of the underlying mission code changed, but it ought to be possible to figure it out again.
Edit: Oh, and yes, they string together multiple missions. They also allow you to make a decision in the conversation tree that then changes which mission comes next. So the storyline can now branch.
I've still only done a few myself, but they show up even if you're on the other side of the map and you get some basic information about them. You can head over to the relevant planet to take them or just ignore them and let them expire. They can be configured with time passing between missions and/or immediate consecutive missions.
Come to think of it, it's probably technically feasible to add deployments back in as the replacement to travel missions that they were before... I assume they aren't working because some of the underlying mission code changed, but it ought to be possible to figure it out again.
Edit: Oh, and yes, they string together multiple missions. They also allow you to make a decision in the conversation tree that then changes which mission comes next. So the storyline can now branch.