So I have two Vigor 2866's at my house in a Hot-Standby High Availability, and when I enable IPv6, I find after a few hours to a day or so, the routers lock up and stop routing IPv4 traffic. (Internet drops out, site-site VPN's go down, can't ping WAN IP from my 2nd home, etc...)

At first I thought It was due to how I configured IPv6 across the two 2866's in the HA setup, but even enabling IPv6 on just the WAN side of the primary 2866* , still causes the same lock up issue.
* That's right no IPv6 enabled at all on backup 2866 and no IPv6 on the LAN and HA settings of the primary 2866.

Has anyone seen similar and maybe know what is causing the issue?

I've had a 3910 stop routing ipv6 traffic due to buggy firmware and it will stop routing ipv4 traffic if I change bind ip to mac after period of time whatever firmware it has.

I would reset it to back default after backing up you're config. Then reflash the firmware then see what happens. What version of firmware are you using? If not the latest updating to that. Or if you already upgraded and then problem surfaced go back to the previous version again after resetting to defaults.