Deleted documents appear in suggestion list

I have deleted documents from an index, but still see them in suggestions. I have tried explicit refresh, but it also doesn't help.
I could track this problem back in 2014 in earlier versions, but it sounds that it is solved in current version, but I'm facing the same problem.

Is there any way to purge a document from an index including suggestions?

This is a well known limitation of older versions/completion suggesters. There have been a variety of issues posted around it. If you search around the for "completion suggester deleted documents" you'll find any number of them, including the issue you linked (but many others as well).

In 5.0, the completion suggester was completely rewritten to take deleted documents into account. See https://www.elastic.co/blog/elasticsearch-5-0-0-released and https://www.elastic.co/guide/en/elasticsearch/reference/5.3/search-suggesters-completion.html for some details. You should upgrade to 5.3+ to take advantage of this!

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@shanec suggestion is right and you should think about migrating to ES 5.3+.

Also follow these migration steps:
https://www.elastic.co/guide/en/elasticsearch/reference/current/setup-upgrade.html

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