On the current rolling releases for VyOS, configuring a flowtable on a bond interface is not reboot safe. On reboot the entire firewall stanza will be missing as it appears that the flowtable attempts to be created before the bond interface is available.
To reproduce, I have a bond interface with VLAN ID 100 configured. I create a flowtable with just the single interface:
set firewall flowtable test interface bond0.100
Save the config and reboot and the problem occurs. If I use a physical interface instead it becomes reboot safe.