I was partied during all of this.
I had two already and cleared an Echo. I got two from the reward and transferred them, they both disappeared.
I have been desynced from the server. I have stability for the boss and after doing the fight, I got no blessing or loot from the boss and my stability did not change. After some echoes, I am not even getting items out of the chest.
I took the two I had left, I used one on a yellow staff and the staff never turned into a unique, it stayed the same. I shut down and restarted and the other Rune of Ascendance is gone.
I am out three Runes of Ascendance now.