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More tests show that it is not network-related (and the test with the RIPE Atlas probes is misleading) since a client machine on the same network has no problem. So, there is only one client with the (still mysterious) problem.
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The machine with the problem was able to talk with other IPv6 DoT resolvers such as
dns.shaftinc.fr
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Restarting the DoT server (a dnsdist) solved the problem. Now, everyone is happy. Since dnsdist had more than two months uptime, I assume there was something wrong in it.
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