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Thank you for your feedback, DNSB!
I guess I know what was happening. Prior to 2.1.0 the index of different libraries was not fully separated. Now once you run 2.1.0 for the first time the plugin will try to upgrade ElasticSearch index to the new "format", where every library has completely separate index. To do so, plugin will attach the index to currently selected library, therefore leaving the index for other libraries empty.
For people who were using only one library this upgrade won't be noticed. But the ones who were already using different libraries they might see some strange behavior.
Of course, full reindexing will fix this issue.
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