Time-based indices generated by Logstash are based on UTC time. Each index will therefore not necessarily contain a full days of data in the time zone you are in. If you create an index pattern just matching a single index, you would be able to see this in Kibana.
Retention is generally managed by deleting entire indices, as this is much more efficient than deleting records individually from an index. You could keep an extra days worth of indices, which would ensure the full time period is covered or possibly modify the index naming in Logstash and override the default to get a date based on your time zone.
Kibana and Elasticsearch require/assume that the timestamp is is UTC, so changing this to something else will cause problems. A better way may be to parse the raw event date and use this to build the index name for the elastic search output.
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