Poor recall in ODFE1.8

After the _update_by_query, I perform a KNN query. The first one times out. When I do it again, I get a response. The document that was previously not being recalled is now recalled, but others are now not being returned. Oddly, after performing this query, now _stats returns something different (again note the changed “deleted” count):

curl -X GET "localhost:9205/research-index/_stats?pretty"
{
  "_shards" : {
    "total" : 2,
    "successful" : 1,
    "failed" : 0
  },
  "_all" : {
    "primaries" : {
      "docs" : {
        "count" : 18632,
        "deleted" : 11632
      },
      "store" : {
        "size_in_bytes" : 1196177467,
        "reserved_in_bytes" : 0
      },
      "indexing" : {
        "index_total" : 18632,
        "index_time_in_millis" : 35866,
        "index_current" : 0,
        "index_failed" : 0,
        "delete_total" : 0,
        "delete_time_in_millis" : 0,
        "delete_current" : 0,
        "noop_update_total" : 0,
        "is_throttled" : false,
        "throttle_time_in_millis" : 0
      },
      "get" : {
        "total" : 0,
        "time_in_millis" : 0,
        "exists_total" : 0,
        "exists_time_in_millis" : 0,
        "missing_total" : 0,
        "missing_time_in_millis" : 0,
        "current" : 0
      },
      "search" : {
        "open_contexts" : 0,
        "query_total" : 48,
        "query_time_in_millis" : 406,
        "query_current" : 0,
        "fetch_total" : 48,
        "fetch_time_in_millis" : 3535,
        "fetch_current" : 0,
        "scroll_total" : 1,
        "scroll_time_in_millis" : 40896,
        "scroll_current" : 0,
        "suggest_total" : 0,
        "suggest_time_in_millis" : 0,
        "suggest_current" : 0
      },
      "merges" : {
        "current" : 1,
        "current_docs" : 30264,
        "current_size_in_bytes" : 524525951,
        "total" : 1,
        "total_time_in_millis" : 48685,
        "total_docs" : 27812,
        "total_size_in_bytes" : 491844979,
        "total_stopped_time_in_millis" : 0,
        "total_throttled_time_in_millis" : 11209,
        "total_auto_throttle_in_bytes" : 17331834
      },
      "refresh" : {
        "total" : 14,
        "total_time_in_millis" : 28465,
        "external_total" : 14,
        "external_total_time_in_millis" : 28682,
        "listeners" : 0
      },
      "flush" : {
        "total" : 1,
        "periodic" : 0,
        "total_time_in_millis" : 0
      },
      "warmer" : {
        "current" : 0,
        "total" : 13,
        "total_time_in_millis" : 1
      },
      "query_cache" : {
        "memory_size_in_bytes" : 2940,
        "total_count" : 43,
        "hit_count" : 5,
        "miss_count" : 38,
        "cache_size" : 1,
        "cache_count" : 2,
        "evictions" : 1
      },
      "fielddata" : {
        "memory_size_in_bytes" : 0,
        "evictions" : 0
      },
      "completion" : {
        "size_in_bytes" : 0
      },
      "segments" : {
        "count" : 5,
        "memory_in_bytes" : 92204,
        "terms_memory_in_bytes" : 63040,
        "stored_fields_memory_in_bytes" : 3864,
        "term_vectors_memory_in_bytes" : 0,
        "norms_memory_in_bytes" : 9600,
        "points_memory_in_bytes" : 0,
        "doc_values_memory_in_bytes" : 15700,
        "index_writer_memory_in_bytes" : 0,
        "version_map_memory_in_bytes" : 0,
        "fixed_bit_set_memory_in_bytes" : 0,
        "max_unsafe_auto_id_timestamp" : -1,
        "file_sizes" : { }
      },
      "translog" : {
        "operations" : 18632,
        "size_in_bytes" : 318730922,
        "uncommitted_operations" : 18632,
        "uncommitted_size_in_bytes" : 318730922,
        "earliest_last_modified_age" : 0
      },
      "request_cache" : {
        "memory_size_in_bytes" : 0,
        "evictions" : 0,
        "hit_count" : 0,
        "miss_count" : 0
      },
      "recovery" : {
        "current_as_source" : 0,
        "current_as_target" : 0,
        "throttle_time_in_millis" : 0
      }
    },
    "total" : {
      "docs" : {
        "count" : 18632,
        "deleted" : 11632
      },
      "store" : {
        "size_in_bytes" : 1196177467,
        "reserved_in_bytes" : 0
      },
      "indexing" : {
        "index_total" : 18632,
        "index_time_in_millis" : 35866,
        "index_current" : 0,
        "index_failed" : 0,
        "delete_total" : 0,
        "delete_time_in_millis" : 0,
        "delete_current" : 0,
        "noop_update_total" : 0,
        "is_throttled" : false,
        "throttle_time_in_millis" : 0
      },
      "get" : {
        "total" : 0,
        "time_in_millis" : 0,
        "exists_total" : 0,
        "exists_time_in_millis" : 0,
        "missing_total" : 0,
        "missing_time_in_millis" : 0,
        "current" : 0
      },
      "search" : {
        "open_contexts" : 0,
        "query_total" : 48,
        "query_time_in_millis" : 406,
        "query_current" : 0,
        "fetch_total" : 48,
        "fetch_time_in_millis" : 3535,
        "fetch_current" : 0,
        "scroll_total" : 1,
        "scroll_time_in_millis" : 40896,
        "scroll_current" : 0,
        "suggest_total" : 0,
        "suggest_time_in_millis" : 0,
        "suggest_current" : 0
      },
      "merges" : {
        "current" : 1,
        "current_docs" : 30264,
        "current_size_in_bytes" : 524525951,
        "total" : 1,
        "total_time_in_millis" : 48685,
        "total_docs" : 27812,
        "total_size_in_bytes" : 491844979,
        "total_stopped_time_in_millis" : 0,
        "total_throttled_time_in_millis" : 11209,
        "total_auto_throttle_in_bytes" : 17331834
      },
      "refresh" : {
        "total" : 14,
        "total_time_in_millis" : 28465,
        "external_total" : 14,
        "external_total_time_in_millis" : 28682,
        "listeners" : 0
      },
      "flush" : {
        "total" : 1,
        "periodic" : 0,
        "total_time_in_millis" : 0
      },
      "warmer" : {
        "current" : 0,
        "total" : 13,
        "total_time_in_millis" : 1
      },
      "query_cache" : {
        "memory_size_in_bytes" : 2940,
        "total_count" : 43,
        "hit_count" : 5,
        "miss_count" : 38,
        "cache_size" : 1,
        "cache_count" : 2,
        "evictions" : 1
      },
      "fielddata" : {
        "memory_size_in_bytes" : 0,
        "evictions" : 0
      },
      "completion" : {
        "size_in_bytes" : 0
      },
      "segments" : {
        "count" : 5,
        "memory_in_bytes" : 92204,
        "terms_memory_in_bytes" : 63040,
        "stored_fields_memory_in_bytes" : 3864,
        "term_vectors_memory_in_bytes" : 0,
        "norms_memory_in_bytes" : 9600,
        "points_memory_in_bytes" : 0,
        "doc_values_memory_in_bytes" : 15700,
        "index_writer_memory_in_bytes" : 0,
        "version_map_memory_in_bytes" : 0,
        "fixed_bit_set_memory_in_bytes" : 0,
        "max_unsafe_auto_id_timestamp" : -1,
        "file_sizes" : { }
      },
      "translog" : {
        "operations" : 18632,
        "size_in_bytes" : 318730922,
        "uncommitted_operations" : 18632,
        "uncommitted_size_in_bytes" : 318730922,
        "earliest_last_modified_age" : 0
      },
      "request_cache" : {
        "memory_size_in_bytes" : 0,
        "evictions" : 0,
        "hit_count" : 0,
        "miss_count" : 0
      },
      "recovery" : {
        "current_as_source" : 0,
        "current_as_target" : 0,
        "throttle_time_in_millis" : 0
      }
    }
  },
  "indices" : {
    "research-index" : {
      "uuid" : "ltZ3Mh2JR2uxnQrPCOg0Ig",
      "primaries" : {
        "docs" : {
          "count" : 18632,
          "deleted" : 11632
        },
        "store" : {
          "size_in_bytes" : 1196177467,
          "reserved_in_bytes" : 0
        },
        "indexing" : {
          "index_total" : 18632,
          "index_time_in_millis" : 35866,
          "index_current" : 0,
          "index_failed" : 0,
          "delete_total" : 0,
          "delete_time_in_millis" : 0,
          "delete_current" : 0,
          "noop_update_total" : 0,
          "is_throttled" : false,
          "throttle_time_in_millis" : 0
        },
        "get" : {
          "total" : 0,
          "time_in_millis" : 0,
          "exists_total" : 0,
          "exists_time_in_millis" : 0,
          "missing_total" : 0,
          "missing_time_in_millis" : 0,
          "current" : 0
        },
        "search" : {
          "open_contexts" : 0,
          "query_total" : 48,
          "query_time_in_millis" : 406,
          "query_current" : 0,
          "fetch_total" : 48,
          "fetch_time_in_millis" : 3535,
          "fetch_current" : 0,
          "scroll_total" : 1,
          "scroll_time_in_millis" : 40896,
          "scroll_current" : 0,
          "suggest_total" : 0,
          "suggest_time_in_millis" : 0,
          "suggest_current" : 0
        },
        "merges" : {
          "current" : 1,
          "current_docs" : 30264,
          "current_size_in_bytes" : 524525951,
          "total" : 1,
          "total_time_in_millis" : 48685,
          "total_docs" : 27812,
          "total_size_in_bytes" : 491844979,
          "total_stopped_time_in_millis" : 0,
          "total_throttled_time_in_millis" : 11209,
          "total_auto_throttle_in_bytes" : 17331834
        },
        "refresh" : {
          "total" : 14,
          "total_time_in_millis" : 28465,
          "external_total" : 14,
          "external_total_time_in_millis" : 28682,
          "listeners" : 0
        },
        "flush" : {
          "total" : 1,
          "periodic" : 0,
          "total_time_in_millis" : 0
        },
        "warmer" : {
          "current" : 0,
          "total" : 13,
          "total_time_in_millis" : 1
        },
        "query_cache" : {
          "memory_size_in_bytes" : 2940,
          "total_count" : 43,
          "hit_count" : 5,
          "miss_count" : 38,
          "cache_size" : 1,
          "cache_count" : 2,
          "evictions" : 1
        },
        "fielddata" : {
          "memory_size_in_bytes" : 0,
          "evictions" : 0
        },
        "completion" : {
          "size_in_bytes" : 0
        },
        "segments" : {
          "count" : 5,
          "memory_in_bytes" : 92204,
          "terms_memory_in_bytes" : 63040,
          "stored_fields_memory_in_bytes" : 3864,
          "term_vectors_memory_in_bytes" : 0,
          "norms_memory_in_bytes" : 9600,
          "points_memory_in_bytes" : 0,
          "doc_values_memory_in_bytes" : 15700,
          "index_writer_memory_in_bytes" : 0,
          "version_map_memory_in_bytes" : 0,
          "fixed_bit_set_memory_in_bytes" : 0,
          "max_unsafe_auto_id_timestamp" : -1,
          "file_sizes" : { }
        },
        "translog" : {
          "operations" : 18632,
          "size_in_bytes" : 318730922,
          "uncommitted_operations" : 18632,
          "uncommitted_size_in_bytes" : 318730922,
          "earliest_last_modified_age" : 0
        },
        "request_cache" : {
          "memory_size_in_bytes" : 0,
          "evictions" : 0,
          "hit_count" : 0,
          "miss_count" : 0
        },
        "recovery" : {
          "current_as_source" : 0,
          "current_as_target" : 0,
          "throttle_time_in_millis" : 0
        }
      },
      "total" : {
        "docs" : {
          "count" : 18632,
          "deleted" : 11632
        },
        "store" : {
          "size_in_bytes" : 1196177467,
          "reserved_in_bytes" : 0
        },
        "indexing" : {
          "index_total" : 18632,
          "index_time_in_millis" : 35866,
          "index_current" : 0,
          "index_failed" : 0,
          "delete_total" : 0,
          "delete_time_in_millis" : 0,
          "delete_current" : 0,
          "noop_update_total" : 0,
          "is_throttled" : false,
          "throttle_time_in_millis" : 0
        },
        "get" : {
          "total" : 0,
          "time_in_millis" : 0,
          "exists_total" : 0,
          "exists_time_in_millis" : 0,
          "missing_total" : 0,
          "missing_time_in_millis" : 0,
          "current" : 0
        },
        "search" : {
          "open_contexts" : 0,
          "query_total" : 48,
          "query_time_in_millis" : 406,
          "query_current" : 0,
          "fetch_total" : 48,
          "fetch_time_in_millis" : 3535,
          "fetch_current" : 0,
          "scroll_total" : 1,
          "scroll_time_in_millis" : 40896,
          "scroll_current" : 0,
          "suggest_total" : 0,
          "suggest_time_in_millis" : 0,
          "suggest_current" : 0
        },
        "merges" : {
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          "current_size_in_bytes" : 524525951,
          "total" : 1,
          "total_time_in_millis" : 48685,
          "total_docs" : 27812,
          "total_size_in_bytes" : 491844979,
          "total_stopped_time_in_millis" : 0,
          "total_throttled_time_in_millis" : 11209,
          "total_auto_throttle_in_bytes" : 17331834
        },
        "refresh" : {
          "total" : 14,
          "total_time_in_millis" : 28465,
          "external_total" : 14,
          "external_total_time_in_millis" : 28682,
          "listeners" : 0
        },
        "flush" : {
          "total" : 1,
          "periodic" : 0,
          "total_time_in_millis" : 0
        },
        "warmer" : {
          "current" : 0,
          "total" : 13,
          "total_time_in_millis" : 1
        },
        "query_cache" : {
          "memory_size_in_bytes" : 2940,
          "total_count" : 43,
          "hit_count" : 5,
          "miss_count" : 38,
          "cache_size" : 1,
          "cache_count" : 2,
          "evictions" : 1
        },
        "fielddata" : {
          "memory_size_in_bytes" : 0,
          "evictions" : 0
        },
        "completion" : {
          "size_in_bytes" : 0
        },
        "segments" : {
          "count" : 5,
          "memory_in_bytes" : 92204,
          "terms_memory_in_bytes" : 63040,
          "stored_fields_memory_in_bytes" : 3864,
          "term_vectors_memory_in_bytes" : 0,
          "norms_memory_in_bytes" : 9600,
          "points_memory_in_bytes" : 0,
          "doc_values_memory_in_bytes" : 15700,
          "index_writer_memory_in_bytes" : 0,
          "version_map_memory_in_bytes" : 0,
          "fixed_bit_set_memory_in_bytes" : 0,
          "max_unsafe_auto_id_timestamp" : -1,
          "file_sizes" : { }
        },
        "translog" : {
          "operations" : 18632,
          "size_in_bytes" : 318730922,
          "uncommitted_operations" : 18632,
          "uncommitted_size_in_bytes" : 318730922,
          "earliest_last_modified_age" : 0
        },
        "request_cache" : {
          "memory_size_in_bytes" : 0,
          "evictions" : 0,
          "hit_count" : 0,
          "miss_count" : 0
        },
        "recovery" : {
          "current_as_source" : 0,
          "current_as_target" : 0,
          "throttle_time_in_millis" : 0
        }
      }
    }
  }
}