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I expected that the update would be written somewhere on a NAND on the motherboard, but the message said that it was written on the hard disk :-)
Your partially right about that...........the update is indeed stored on the hard disk, but when it is installed, it will proably write to the NAND and keep the FW there.
What you should try, is get a PS3 that hasnt been updated from the 1.00 FW and put a blank HDD in the PS3, so it wont find the update to install.