I think I need a bit more information from you: how did you upgrade? Do both Kibana instances have a unique uuid? (You can find the uuid in the location of your kibana.ymlpath.data, default is a folder called data) Did any other settings change in kibana.yml?
Finally I found a topic with the solution : stop kibana on one of the two Kibana server, remove /var/lib/kibana/uuid and restart. This will create a new uuid.
So I think documentation can be updated to integrate this setting
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