In fact flashing using ATIWinFlash (in command line) worked well in itself.
The problem was that I did not understood well the procedure to flash-back the first one after putting a non working one.
First time I tried to flash, I had booted on bios 2 (the one I do not normally use) and it told me it was write protected.
I falsely deduced only the first one could be flashed. I rebooted on bios 1 and flashed it.
After discovering it was not working, I rebooted on bios 2 and reflashed ... but forgot to press the button while the computer was already booted up ... and ended flashing another non-working bios
It was kind of un-natural to me to use a jumper on a powered board ... Besides, the first complain about write protect was in fact due to the flashing software not running in administrator mode.
By the way, I managed to get my board working again by booting on an old PCI card, so no harm in the end, but still some cold sweat ^^
Only flash in DOS using a bootable DOS USB stick. Do not flash in Windows.
Do not flash your number two BIOS. Only use your number two BIOS if you mess up the first one. Make sure you make a backup of your original BIOS using GPUz.