Thank you a lot for the tip! It does work!
You were right the file is reset by Nickel on each startup.
I ended up implementing this ugly workaround, replacing the last character everytime I want to launch Plato, Koreader, or my own app with NickelMenu:
Code:
menu_item :main :Plato :cmd_spawn :sed -i '$s/.$/4/' /mnt/onboard/.kobo/version
chain_always :cmd_spawn :/mnt/onboard/.adds/plato/plato.sh
Hoping a future update fixes this!