Avanti emulates the Alphaserver 400/166 and its boot variables behave exactly as the real Alphaserver.  To save the current boot variables between boots, ensure the emulator writes them to the NVRAM file via an exit.

>>> set bootdef_dev DKA0
>>> set boot_osflags 0
>>> exit

While running, Avanti saves the NVRAM contents to the NVRAM file approximately every 10 seconds.