Hi, some of those files are there for the FS (file system).
don't format it!
The flash file system changes depending on it being a "slave drive" (/mnt/...) or / (not /root).IMHO
An unusual bug I have come across, with flash to HDD installs, is you need to keep a working copy of the /boot/grub dir someplace safe from (install)system-formats. ie, a different partition.
Because what occurs is that the boot loader (or Grub-install) does not get written to /boot.
So you may need to do that with an app, like with... Grub Legacy boot loader, Grub4Dos...
or edit the file yourself
sh-4.1# cat /boot/grub/menu.lst
# GRUB configuration file '/boot/grub/menu.lst'.
# generated by 'grubconfig'. Mon Oct 1 18:15:13 2012
# The backup copy of the MBR for drive '/dev/sda' is
# here '/boot/grub/mbr.sda.14773'. You can restore it like this.
# dd if=/boot/grub/mbr.sda.14773 of=/dev/sda bs=512 count=1
# Start GRUB global section
color light-gray/blue black/light-gray
# End GRUB global section
# Other bootable partition config begins
title Windows (on /dev/sda1)
# Other bootable partition config ends
# Linux bootable partition config begins
title Studio-1337 Linux
kernel /boot/vmlinuz root=/dev/sda3 pmedia=atahd vga=785
# Linux bootable partition config ends
After quite a few tests, I do this now
soon I'll have a script to set my settings after a clean install.
Hope this helps, Glenn (Late one afternoon)