On my device, I had first to re-formatted the NAND, allowing 500 Mb (instead of 256 Mb) to the Android system partition and 900 (was 750) Mb to data/cache. The "media" FAT partition is automatically reduced.
I did this by using the "install3.sh" setup script (see here:
https://github.com/Renesas-EMEV2/Bootloader/blob/emev-4.1/fwupd/files/install3.sh lines 132 and 135), putting it into the SD card home, renaming it to "install.sh" and then removing (renaming) "ff4" from the same dir.
This way, the flashing procedure will use the install.sh script, in place of the interactive program ff4, and will reformat the NAND before flashing the new firmware.
Let it go, as it takes time (few minutes)... no message will appear on screen until the final confirmation.
The following re-flashing (even using ff4), will keep the new partitioning scheme.