flash.sh is never on the Jetson. This is part of the “driver package” which runs on the host PC. The driver package itself understands a Jetson in recovery mode (which turns it into a custom USB device), and is normally installed on the host PC by installing JetPack/SDK Manager.
Since you can get to the login, could you remove unused files elsewhere to start with? For example, anything in “~/Downloads” of the Jetson. Perhaps something in “~/Documents”. If not, then do you have anything valuable you are trying to save? I ask the latter because an eMMC model can be cloned, the clone can be edited, and then the flash can take place with the clone, but this is time consuming.