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Custom KV store isn't just a SQLite file, right? Because there are tools for that
Since it sounds like you have to rebuild from scratch, you may want to consider RFC 2136 for Dynamic DNS, and DNSControl for everything else. You could even just roll DNSControl with a custom web script and Cron if you want to skip RFC 2136.
After that, all you need to do is to spin up a new DNS server (I can recommend PowerDNS) and fill in the recovered data. I think it shouldn't take longer than a few days to do all this.
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