OFSO,
Do you realise how much time this would add to your shutdown routine.
A better use of your time and effort would be to script a scheduled startup to occur in the middle of the night, spend a couple of hours doing a backup to your flash drive (for your own good, please use off-the-shelf rather than trying to reinvent the wheel with batch scripts unless you know what you're doing - i.e. correct exception handling for a start ! ) and then shutdown your computer again.
Option two is to reformat your primary drive and to do software RAID1 between the data partition on your primary drive and a partition on your flash drive.