In another thread somebody suggested me to try the chambers dictionary on the CyBook. Well it crashes my CyBook. Is it because it is build 476?

If so, my problem is that I cannot upgrade since the SD card is not working. But I've got the idea that I can try to copy the system folder from a system of build number 538, is that possible?

Yes, crashing on dictionary lookup (for some dictionaries) was a bug in build 476 which was fixed in 538.

I'm afraid that copying the system folder isn't enough; you really do need to reflash the firmware. Looks like your Gen3 needs to go back to Bookeen, I'm afraid.