I'm still amazed at how primitive long term archival systems are at the moment.

Does anyone know a tool/solution that keeps two logically independent sets of archives, plus integrity checksums with the metadata?

Borgbackup is close, but it has no mechanism that I can see to detect changes in the source. Detecting changes in the archive is useless without a second valid copy

It's a bit like finding out that symmetric cryptography isn't[1] a robustly working thing.

[1]: imperialviolet.org/2015/05/16/

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What I mean by "two logically independent sets of archives + checksums" is the ability to store data in two independent systems, where the integrity checks are applied on BOTH (one system can be the original files on a desktop computer), so that when silent data corruption is detected there is at least one pristine copy to restore from.

Most backup tools just take bitrot induced changes from the source and propagate them to dest, eventually removing the good data once old snapshots are removed.

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