Increase PWM bit resolution on only one timer 2 output
As long as you don't use PWM (i.e. analogWrite) on pin 9, any changes made to timer1 won't affect pin 9.

It will change both outputs, as both use the same (single) timer.

But you can use code to convert a 8-bit PWM value to a 16-bit value by simply multiplying the 8-bit value by 256.