"That is mx.screen.refresh(). It refreshes the main form but not a popup form."
To be precise, it refreshes the view in the main content window. This call was never meant to refresh anything outside that. From the API docs, http://apidocs.mendix.com/client/screen.html#refresh ,
This method is called to refresh the current form in content.
Granted, this could use some more elaborate description.
change/refresh calls made from a Microflow to the client send specific instructions back to the browser for cache updates, update messages to subscribed widgets, etc.
The unfortunately named method 'objectPing' should send a message to all subscribed widgets - can you reproduce this in a test project and send it to the support portal?