I'd have said changing system_stm32f4xx.c is what you need - not sure why it wouldn't be taking effect.
You could have a play with http://www.espruino.com/Reference#l_E_setClock - it'll allow you to play with prescalers on the fly so at least you can test and see if it's doing the right thing
Espruino is a JavaScript interpreter for low-power Microcontrollers. This site is both a support community for Espruino and a place to share what you are working on.
I'd have said changing
system_stm32f4xx.c
is what you need - not sure why it wouldn't be taking effect.You could have a play with http://www.espruino.com/Reference#l_E_setClock - it'll allow you to play with prescalers on the fly so at least you can test and see if it's doing the right thing