Okay first thought. It's a DX so If you trash it it's a problem.
second thought. I'm fairly sure I saw something a bit like this in one of the font threads. don't shoot me if I'm wrong, so maybe have a rummage around in there. IIRC it was some sort of configuration tool. Unsure if it was for a DX.
In other news have you considered not rebooting the device entirely.
Since you clearly have root access to the device is there not a way to more gently massage a restart - or even better maybe just cause the bookreader process to re-read the value - perhaps via killing/restarting its process.
Anyway they are all idle thoughts utterly unbacked up with any facts. I do have a dx. Cost a fortune, no way am I bricking it to try to get nicer font sizes. not until I can recover it no sweat.