In my case the quest vanished as i started own kingdom, along with the companion and the troops i had sent out on quest.
However companion was still visible in the clan window, and by the looks of it she had resetted to the settlement defined as her hometown. That one I solved easily by making her governor for one of my fiefs and picked her baack up.
My point here was that the quest shoud not reset when accepting the main quest, nor should the companion and troops you have out on active quests simply reset or disapear. I checked if the troops was sent to any of my fiefs, but it wasnt. I had sent out max tier troops so i knew what to look for, was imperial bucellarii