Use -autoconfig, then put host_writeconfig into the console so the blank config get's saved (otherwise the game might revert to your previous config after removing -autoconfig).
Then remove -autoconfig, start the game again, change settings, binds etc. how you want them and use host_writeconfig again.
The reason your binds don't save is probably because you forgot to remove -autoconfig from launch options, so the game loads a blank config every time.
That said, you won't necessarily get a noticeable FPS boost switching from rhapsody's to comanglias.
The difference between the two isn't huge and depending on your PC it might not give any more FPS.
Also, if you just run the new autoexec, most of the commands should change without using -autoconfig.
The reason you should use -autoconfig is because if the old config uses commands that the new one doesn't use at all, those commands won't change with the new config.
I don't think there's a way that your game could get stuck on the old config entirely.
All the commands that are in the new config will definitely get changed.