So I did something in the new x-pac that broke the game for me and I am going to post what I did here so you wont be like me. I will try and remove as much as the spoiler content as I can. The below steps basically removed companions from the game, on all characters, across all servers. I have submitted a bug report, this is just a PSA to not be dumb like me.
I did this in Chapter IV using the companions listed, though I am sure doing this general flow of actions with others in other points of the story will produce similar results.
1. With HK55 as companion while clearing the gravestone ship I sent Lana out on an underworld trading mission
2. Completed quest to clear out gravestone, and selected to go with Lana to find food and water, WHILE she was still on underworld trading mission
3. She is supposed to be your active companion, you are unable to summon her as she is still in the underworld.
4. Upon timer for mission ending she does not return to your side for the quest.
5. You are also unable to summon any companion, on any character, at any stage of the game, on any server
Customer Service was unable to assist me and stated it must be fixed in a future patch.