How do you know that the ISP replacing it often is "unusual, to say the least"? Or is that something you know?
Even my incoming rdiff-backup jobs don't raise a noticeable number of errors.
If 30-minutely prefix changes were common, people would definitely be complaining about it.
...but okay, I won't claim that I catch everything. Can I ask which ISP this is, or at least which country? Perhaps it's common in places that don't have much presence in the English-speaking parts of the internet.
It's nice to hear that it mostly works for you. It should do, but a lot of software is terrible at handling dynamic changes -- it seems to be something that programmers struggle with. The biggest problem should be that long-running connections aren't possible.
Changing your prefix every half an hour would be... unusual, at least, although again I wouldn't put it past some ISPs to do that (possibly unintentionally)... but sounds like your prefix might be changing every time you do a DHCPv6-PD request, which makes me wonder if your DHCPv6 client might be generating a new DUID for every request rather than remembering it.