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.
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.
Both of my ISPs hand out new ISPs hand out new /64 prefixes every so often. One does it every half-hour, the other is comparable but I don't remember. I think they do it to encourage business customers to get more expensive connections, but the effect on my connections is that each device's IP address changes every few minutes, within the ISP's /32, and doesn't repeat in a year... and I do wonder how many IPSs do this.