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The problem is that the peer being unregistered is not aware that it is being unregistered, and is still trying to connect to the peers that it is part of.
If you wait after unregistering, it does become unavailable, it just doesn't have time to execute the transaction in attached example.
What we really have problems with is peer registration, since I can neither re-register peer after unregistering it, neither register a new peer. #2060 is also kind-of-invalid, since the new peer added there isn't configured to trust any of the others, so it refuses to connect when they try to, which sounds like expected behaviour. Unfortunately, if you add other peer's to new peer's configuration, it joins the network, but fails to sync blocks.
As far as I understand there are two, maybe three issues here - something I/O related that makes reconnecting peer after unregistering and re-registering it fail and some problems with block sync, which prevents new peers from syncing by failing validation. There may be is a third problem connected to actors, but I think while they aren't failing gracefully, that's not the root cause here, so I'm currently concentrating on the other two.
MWE
Install Iroha 2 java SDK.
run
https://gist.github.com/arndey/98c5b2bb300c13304beba53eca9e2882
Reproducibility outside docker
Reproducible.
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