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).
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