Fields disappear after refreshing on visualization pages

It looks like you're hitting Kibana and/or Elasticsearch's max payload size. These are configurable via Kibana's maxPayloadBytes and Elasticsearch's http.max_content_length.

But it sounds like you're saying this large number of fields is unexpected? I notice your index pattern is just *. Are you casting too wide of a net and including indices that you don't intend to perhaps? If you look at the response to the GET request for <kibana-url>/elasticsearch/*/_mapping/field/* (before the one that fails) you can see all of the fields from all of the indices that are getting pulled back.