That's wat I have done for now, however this functionality should come available soon.
I've raised a case with support regarding this issue.
"Unfortunately, GeoAnalytics extension does not support printing. This limitation is mainly related to the current multi layer architecture of overlaying charts and data in GeoAnalytics. The multi layer architecture makes GeoAnalytics a very powerful, fast and flexible product where the primary focus is. However, the printing process requires each layer to be handled separately during printing. This limitation will be resolved and printing will be possible and supported in a future version of GeoAnalytics and Qlik Sense within the product development map, but unfortunately no timeline has been set up yet."
I'm facing the same kind of issue : trying to export to pdf a story containing a map. Everything goes fine except for the map that doesn't appear in the pdf when exporting from the server (it works perfectly when working with desktop version)
I'm using Qlik Sense version April 2018. Do you knw when the limitation was resolved in the release of june 2018 ? or is it still pending ?
Many thanks for your answer.