If you save a ship with a different name or rename a ship, then upload the file to discord and drag it in game, the in game name can be different from the file name. the ship file attached should be an instance of this.
#Ships revert to previous name after uploading to discord
radiant ridge
cedar pawn
Are you renaming the ship file directly?
Basically, Cosmoteer gets the ship name from the filename, but if it can't do that then it falls back to the name stored in the ship data itself. When you upload a ship file to Discord, Discord randomizes the filename, so it has to fall back to using the name in the ship data.