You will need to edit the mongodb input plugin ruby code in your logstash installation.
it will be in E:\Elasticsearch\logstash-6.5.4\vendor\bundle\jruby\2.3.0\gems\logstash-input-mongodb-0.4.1\lib\logstash\inputs\mongodb.rb
you need to go to line 294 (a blank line) and paste the snippet below into the blank line.
elsif v.is_a?(TrueClass) || v.is_a?(FalseClass)
event.set(k.to_s, v)
With ^ this change you don't need mutate/convert (boolean) on any boolean fields any more.