Just read carefully, it says wait till the Omega led stops blinking. After downloading the Firmware it will be copied on the right place and the Omega is starting again. The led will switch of and switch on again and blink till firmware is ready in the Memory.
It could be that the Omega not gets online automatically after update. But in this case you can connect it with USB over serial. A how to, you find in omega.io/getstarted
With wifi you start the wifi Adapter and with wifisetup you can choose the right wifi network again. As you can store more than one wifi-network, it will be probably deactivated after update.