"ipv6 address from-pool" lost after reboot

[DarkNate]

Using a single pool is not an option here. We have a few thousand devices and each has it’s own fd10:x:y:z::/64 prefix. In certain environments, we need an additional network that we can advertise to hosts, and this can’t be in the fd10::/16 range.

This sounds like a problematic approach, IMO. I’d suggest giving this a read and re-doing the design:
http://forum.mikrotik.com/t/how-to-edge-router-and-bng-optimization-for-isps/150007/1