Hello, we can reproduce this bug. We have configuration like this: auto vlan992 iface vlan992 inet manual bridge_ports bond0.992 bridge_stp off bridge_maxwait 0 bridge_fd 0
bond0 is the management interface (with IPv4 and IPv6 addresses). bond0.992 is not explicitly configured anywhere.
On Stretch (bridge-utils 1-15.13) the if-pre-up.d script will call the create_vlan_port() function with port="bond0.992" and inside the function the "dev" var will become bond0. So the function turns off IPv6 for the interface.
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