You are right, that corrupted files in the userspace should not affect the systam stybility. I assume this is not nromal, and if such problems are detected, they will be fixed.
And i can say for a fact, that in all the Cybooks that we sold so far, this was the first time, that we had to reflash a device.
For the reflashing instructions not beeing on the Bookeen homepage: This is due to the fact, that the tool is still under development and is not yet ready for public use and it could possibly still go wrong