I have done the missions for Rhys and Haylen 3 times each without progressing with Brotherhood. I remember going to turn in a mission for them and heard a Virtabird fly overhead. By the time I actually heard it, I was already entering the police station. I quickly went back outside and saw no virtabirx in the sky. Went back in and Danse gives no missions, Rhys an Haylen send me on the same missions, and Military Frequency AF95 is empty static. I also have no missions at this time at all related to the Brotherhood of Steel.

So, did my game glitch, forcing me to abandon my lvl 27 character? Cant reload an autosave as my autosaves are after this happened. I just hope I just missed something.

You just need to progress through the main mission, and it will give you all the brotherhood of steel quests. Until you progress further with the main storyline, the missions from Rhys and Hayden will continue on and on.