This is an easy fix. Format your flash drive. Then download Rufus program for USB flash drives, create an ISO from your ISO file and Rufus will make it bootable without restricting the other space of the flash drive. I have a Windows 7 ISO I keep in a SanDisk flash drive and I can download and copy other files too there. Anytime I want to install Windows I do from this USB and it starts. Other files in the USB don't hinder the installation.