I have just had an email from Private Division support about this issue, reply may be of use:
"I'm sorry to hear that you've encountered a bug where your companion has been marked as dead in the quest log, despite them still being alive.
From what we've discovered, this bug can happen when your companion is climbing a ladder while you start a conversation with an NPC. This causes the companion to continue climbing the ladder forever, and then meet an untimely death when the conversation with the NPC ends. Make sure that your companions are not climbing any ladders before you enter a conversation and this should hopefully prevent this bug from happening to you again until this bug has been resolved. Please note that we currently do not have an ETA as to when this issue will be fixed, but we are actively looking into it.
Sorry for the trouble, and please let me know if you run into any other issues."