Playing on Supernova difficulty. Glitch occurred some few hours ago when I went to Groundbreaker with Nyoka in the party. She spawned downed, repeatedly. Revived her with the inhaler perk, played 5 more hours then realised her quest was botched because it thought she was dead (it says that she's currently occupying her own grave). 

Suggestions:
Fix the spawning bug on Groundbreaker
Fix the quest being flagged as botched for her going down, rather than her actual death.
Have a quest notification to let you know when quests are botched. 

Additional request: 
Console command to reset the quest so that I can complete it without losing 5 hours of progress. (Would also be helpful for others with this issue.) 

When talking with Nyoka at the bar I recieve no additional dialogue options after acquiring the pills. I know I can skip her and go to the destination but I do not want to miss the companion opportunity.