I doubt there would be logs stored in FW prior to 3.50 in an area that remains even after a format/restore. You have to remember that in those firmwares, they did not know about the JB method and probably did not include a check. I would assume that it is perfectly safe if you restore and format the HD. Anyone else got thoughts on this?
When you say there is software, do you mean if you plug in the USB Break 1.1 to your PC, there is software on the storage medium that allows you to choose a payload?