I have been through same issue on 7 clean playthroughs. Followed different paths to get to a continue, and or end of content. As yet on 8th now awaiting next set of content to hopefully push game past those 2 parts. I posted same issue, and some of the steps. Spoilers might have been added, but same result. I did Shani zone quest last after all other content, and then I did her mission(including all 3 in zone staying in cabin, leaving right away, Industrial section, etc..) So far and I have had replies showing at least Shani's Queen part can be updated to a to be continued after zone, Abraxas and Raiders, and Mutants as well as side quests to be continued. I managed on 7 different playthroughs with variations on answers, paths, and order of events still get stuck on those same 2. Both still say spend time with Shani, and I have gone in varied order gone to living room, then Shani's room leading to scene in Library. Which if all other missions and quests are on to be continued should net you visit palace for Queen's part to get it to continued, and get a end of content? I hope that makes sense at least rambled a bit?So I seem to either have a bug, or something just isn't apparent.
Both my remaining quests, "Her Majesty" and "Til Death Do Us Part" say "Spend time with Shani". I have spent time with her. Talked all possible conversations. Worked out with her, and chose all possible options. Nothing updates.