With IPv4, I only have 1 external WAN IP address, so the DDNS update can be done at the router level. But with IPv6, I can have 5 servers with 5 different external IPv6 addresses.
Since most providers dont provide static IPv6 yet, whats the best way to update my AAAA entries at the DDNS provider? Do I run separate update bash scripts on each of the servers? And aside from setting up a cronjob for the update, how do I detect when the IP changes at the server level so I can trigger an update?
Your DDNS provider should have a URL API to update an A or in your case, an AAAA record.
Not all support this yet. I can affirm NameCheap Dynamic DNS only supports ipv4 still. Maybe someone knows of such a domain registrar that supports this?