^Flash drives not detecting shouldn't be indicative of an HDD failure - there was probably a problem within your Windows which was reset when you did a reinstall onto the new hard drive.
Check if the flash drive is shown within either a) the Windows Device Manager, or b) the system BIOS. If both of these fail, then the hardware itself isn't being detected, has likely failed, and you're out a flash drive. Unfortunately, flash drives fall into the same catagory as disc drives these days - cheap for the sake of being cheap; it's a good idea to always keep a backup copy, as things like this do happen.
If the drive is detected, we can go from there, as it may have either been damaged by improper removal (there is a grain of...