I was just attempting this as well and came here looking for an answer! I was not able to migrate the content through ArcGIS Online directly. I did a quick test to see if the updated ArcGIS Assistant was able to handle this process and for a bare bones StoryMap, it was able to copy the content between organizations. This does assume you have a login for the other organization (which defeats the purpose of a Partnered Collaboration)
If you are short on time you could try this out until we get an official response from ESRI. The ability to change ownership from one organization to another through the collaboration is functionality I really hope is possible!
