I have 2 accounts with 39 characters. Over half of these characters can no longer select the Raven mission from the ship's Mission terminal.

This is what I got as response from my ticket:

I am sorry to hear, that you had no chance to start your Revan story but Starting KotFE will auto-completes all previous core game missions, including Companion missions and previous Addons like Revan, you get twice warned of this when clicking to pick up this mission.

What BS. These characters had never selected that damn mission.

I have been here along time and stuck with it all and now thia.... It SUCKS and seems to show the people that run this WONDERFUL game could care less about the USERS.

Am very pissed

I have 2 accounts with 39 characters. Over half of these characters can no longer select the Raven mission from the ship's Mission terminal.

Summary: It is what it is. If you start KotFE/KotET/JUS, you lose access to some parts of the earlier story. It has always been like that ever since KotFE was released in October 2015.

The CS answer is correct but incomplete. If you start KotFE (meaning "take Chapter I: The Hunt from the mission console" *or* "launch that chapter from the Chapters menu") *or* if you skip over KotFE and instead start (historically) KotET ("take Chapter I: Wrath and Ruin from the mission console") or (currently) Jedi Under Siege ("take Inflection Point from the mission console"), it autocompletes all not-yet-completed "critical path" earlier content:

* Class story (from the starter world up to but not including Ilum)

* Class companion stories

* Prelude to Revan / Forged Alliances

* Shadow of Revan (Rishi/Yavin)

* Rise of the Emperor (Ziost)

If you skip past KotFE, all of the above applies *and* KotFE is also autocompleted with default choices based on your faction, but can be replayed (without the possibility of altering the choices).

If you skip past KotET as well, all of the above applies *and* KotET is autocompleted in the same way as KotFE.

Last piece: The game offers plenty of warning if you try to start these things. It's a little clearer if you try to start JUS, but there are enough warnings that they should have given you pause, made you think, "Maybe I should hop on the forums and ask what that means..."