Hello,
in case you did not do so yet, please write back your backup.
I am not exactly sure what went wrong in your case. The bad timing might be part of the problem. Do you run some additional programs that heavily use the CPU while running flashrom? Can you please provide a verbose flashrom log while it is probing only (by adding "-o logfile.txt" to the command line) and please also provide the output of "lspci -nnv".