What version are you upgrading from?
What permissions does the user have when the index pattern field refresh occurs? Do you see any errors in the kibana or elasticsearch logs?
Is it possible for you to provide a har file of the failure to refresh the field list?
You could also try requesting the field list via kibana dev tools using the field caps api which is the underlying mechanism producing the field list - https://www.elastic.co/guide/en/elasticsearch/reference/current/search-field-caps.html
Aside from the error, everything else I see is correct.