ocnbrz' advice is solid. I lost the USB on my launch day Evo earlier this week. I needed to get the phone unrooted in order to get it replaced. I transferred in two steps with a reader; first copied over the s-on tool, flashed it a few times (still showed s-off), then copied PC36IMG and flashed from HBoot. HBoot reported s-on after after that.
Based on my experience, unrooting is a wise move, but be sure to get rid of any root/unroot files, ROMs, flashable zips, root app folders, etc.
Took it to a Sprint store, the tech didn't check for root, but he didn't have any Evos in stock. He found one at a store nearby, and that tech did look for root.
I was careful to swap to an old card with no traces of root apps or files, but I suppose a nearly year old Evo with bone stock screens and zero user installed apps is kind of a dead giveaway in and of itself.
Good luck.