If none of the other methods work, there are three possibilities:
You must remove or desolder the flash IC before you can flash it. It's recommended to solder a socket in place of the flash IC.
When flashing the IC, always connect all input pins. If in doubt, pull /WP, /HOLD, /RESET and alike up towards Vcc.
If you are a developer, you might want to use an EM100Pro instead, which sets the onboard flash on hold, and allows to run custom firmware. It provides a very fast development cycle without actually writing to flash.
It is possible to set the onboard flash on hold and use another flash chip. Connect all lines one-to-one, except /HOLD. Pull /HOLD of the soldered flash IC low, and /HOLD of your replacement flash IC high.