One important note in the start of this thread. @MadMartigan backed up their Xenium flash image first, which was also named flash.bin, and FTPd that off the console before trying to flash anything. That is a critical step before writing any new flash image to your Xenium modchip.
After having their backup, off the xbox in a safe location, they went about trying to flash PrometheOS.
This also isn't really a PrometheOS problem. This is a documentation issue sort of. The Xenium Tools app is very self explanatory but you really need to pay attention to the prompts and text on screen to understand what is happening. MadMartigan was just continually writing their original xenium backup over their chip's flash memory.