I'd imagine that since you changed the name, it got saved as a different .customracexml, so the game doesn't "know" it's the Thalans anymore
This made sense when I first read it, but yesterday I had a diplo message from the Torians that said: "
The Thalan have always been friends to our people.
The Swarm is gradually destroying our civilization. We plead for any help..." (emphasis added)
The Swarm is the name I use when playing as the Thalans. Because of what Kryo said about the game not "knowing" that I'm trying to play the Thalans, I picked the opponents for my current game and left the (other) Thalans out of the game.
This message came up right after about half the galaxy declared war on my Terran allies (for reasons mysterious to me), so I honored my alliance and declared war on them. Now the Torians are asking me to help protect themselves from me? This has got to be some kind of glitch, even if I'm not naming the problem correctly.
I have a screencap and a save game from just after I finished processing the turn.