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Okay, having slept on this I managed to fix it.
My mistake was trying to assign two separate AWS subnets with IPv6 /64 CIDRs to the same VPC and then route one to the other. Instead you just subnet a /64 further into a /80 on the instance itself, and add the /80 as a network interface IPv6 prefix which causes traffic to be routed to the instance.
There's not a great deal you have to do in the VPC other than assign an AWS /56 IPv6 CIDR.
Then in the VPC subnet you can decrease this to a /64 if you want. That's it, you don't have to mess with the Route Table. I would prefer to see the network interface IPs being added to the routing table, because that is what is happening in the background.
So I ended up with:
AWS Instance Network Interface:
IPv6 address: blah:a400::a
IPv6 prefix: blah:a400:1::/80
Instance host external interface ens5:
inet6 blah:a400::a/128 scope global dynamic noprefixroute
inet6 fe80::88:7bff:fe22:587f/64 scope link
Instance host internal interface lxdbr0:
inet6 blah:a400:1::1/80 scope global
Instance host routing table:
blah:a400::/64 dev ens5 proto ra metric 100 hoplimit 255 pref medium
blah:a400:1::/80 dev lxdbr0 proto kernel metric 256 pref medium
default via fe80::d3:52ff:feda:e453 dev ens5 proto ra metric 100 expires 1790sec hoplimit 255 pref medium
Instance container interface on lxdbr0:
inet6 blah:a400:1::a/80 scope global
Instance container routing table:
blah:a400:1::/80 dev eth0 proto kernel metric 256 pref medium
default via blah:a400:1::1 dev eth0 metric 1024 onlink pref medium
Then you can add another /80 IPv6 prefix to the same instance/network interface if for example you needed to use docker and lxc on the same instance:
blah:a400:2::/80
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