What you are suggesting is a pause/resume funtion or save state feature on shut down. Not a bad idea at all, but I am pretty sure it won't be found in 2.0. I think the negative is that the scan, if not completed in one pass is invalid as an infection could be introduced and not caught because past 1 of the scan declared a file clean, yet it was infected after being scanned, but before the part 2 scan completed. So you'd get a false report. Like Jim, I am not aware of any virus scanner that has a pause/resume. You can stop and restart, but never resume - as far as I'm aware.
-steve