Same issue here. I had ElasticSearch and Kibana running with WinlogBeat and Heartbeat sending data to Elasticsearch for about 2 days. I had the index Pattern setup and the Heartbeat dashboard working.
I then install x-pack and they no longer show data.
I decided to delete both the winLogbeat-* and the heartbeat-* indexes from Kibana hoping to recreate them and now Kibana (under Management, Index Patterns) says "Couldn't find any Elasticsearch data".
Here is a print out of my _cat/indices?v
health status index uuid pri rep docs.count docs.deleted store.size pri.store.size
green open .watches bE3Lgf64RAWbIjDB9Fvzdw 1 0 6 0 109.5kb 109.5kb
yellow open winlogbeat-6.2.2-2018.02.27 HzeZJ60BRGaPtY73iIQh_A 3 1 261 0 386kb 386kb
green open .monitoring-kibana-6-2018.02.28 otP9zcAtTBaUlbMgaAh90Q 1 0 1314 0 479.9kb 479.9kb
green open .kibana 0X29PuB2T9Wewbv6LYBIbw 1 0 8 0 22.5kb 22.5kb
close .watcher-history-7-2018.02.27 HjtfVtelTSCeHHGOTeIGtg
yellow open heartbeat-6.2.2-2018.02.28 P_n9wIFRSK-S_XSuJhH0Fw 1 1 12953 0 4.1mb 4.1mb
green open .watcher-history-7-2018.02.28 EbW5DGEoTqS4qR-daSZc6w 1 0 2372 0 3.5mb 3.5mb
yellow open heartbeat-6.2.2-2018.02.27 OX2fK8UpQkK7V56B7wETjQ 1 1 457 0 127.4kb 127.4kb
green open .monitoring-es-6-2018.02.27 UZTXaTYoRh6Ghrk_XyHzOw 1 0 1064 12 683.4kb 683.4kb
green open .monitoring-es-6-2018.02.28 _jYbGX7YRqGGcw6zmX6C5w 1 0 30189 200 17.9mb 17.9mb
green open .monitoring-alerts-6 NYagRVGsTkW1DC11OdA90Q 1 0 4 1 30.5kb 30.5kb
green open .security-6 2esDuIDERNSUg7cgYIcFCw 1 0 3 0 9.9kb 9.9kb
green open .triggered_watches IrsUvtdqS_GsxSOjrU2t8Q 1 0 0 0 144.9kb 144.9kb
yellow open winlogbeat-6.2.2-2018.02.28 nGSBJiE4T2amkAYGIbwo9w 3 1 177 0 449.6kb 449.6kb
Open to any suggestions
In the past when this has happened I did an uninstall of the x-pack and it worked again.