For some reason or another, the program fup is not compiled. The sources should be in X/flash/flash_tools/fup.src.
The easiest way to solve this is to delete the complete directory flash, and run make update (you will lose a image built already). This will restore the flash environment.
As an alternative in directoy X, remove the directory flash. The execute: git clone https://github.com/Audioniek/flash.git flash <Enter>. This will retain a image already built.
Regards,
Audioniek.