You are welcome.
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installed the 505 bios but it only goes into the menu and then
automatically pops up the firmware upgrader the first time the usb is disconnected after a full format of the main drive.
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After format of the main drive there shouldn't/couldn't be a firmware-updater as the updater is a AUTORUN program based on "autrun.js" and "autorun.xml" in /Sony Reader/software/
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Would it be relatively safe for me to use command prompt to recreate the master partition record using diskpart and see if that fixes that particular problem?
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Can't recommend this, as I'm absolutely out of my depth, but as the drive presented as "READER" to the host is only the branch \Data\ of the readers file-system, I'm not sure if you can reach the master partition record via USB.
Most probably you would have to use a startup/autorun script to let it be done by the readers embedded Linux.