You can flash the eMMC the same way you would on a Raspberry Pi IO Board. There are basically 3 steps:
- boot into flash mode by pressing the flash button in the bord while powering the board (or adding a jumper on the connector labelled “eMMC Flash” on the board itself). Holding down the button while powering the device can be tricky. You might want to try a few times. The jumper solution is easier but you have to have access to the board.
- Set the CM4 in USB Mass Storage Device using the rpiboot utility. Note this will vary depending on your OS.
- Use Balena Etcher (or other tools) to flash the image.
I understand you are having issues on the first step above. Correct?