What is happening:
Swift disappears sometime after talking to her the second time and going on to work with Midnight and Hullabaloo, and talking to Olga replays the scene where you bring medical supplies to the pair, before sending the player back to Pyrite. The quest journal refreshes the talk with Pyrite first encounter, but Pyrite refuses to talk to the player at this point.
What should be happening:
Swift should be giving the player the violin to return to Midnight. Pyrite should still be all gung-ho about dirt and statues.
Steps to reproduce the issue:
A really complicated circle of glitches and patches.