You have to update each battery after updating the AC and remote. To do so, plug the bird into your computer, open DJI assistant then click refresh on the update tab. It's funny, it seemed like it just stopped near the end. And I was unsure if it updated until I put the battery in the bird and powered everything up. All was go.
Then just to see if it knew the difference, I put a battery that I had not updated into the bird and powered up. Got a warning immediately that said, "Cannot Take Off" . Clicking on that warning it changed to "Mismatched Firmware, update battery".
This seems to lend credence to the belief that this firmware update is directly related to batteries and / or problems that were present within them. Never expect DJI, or any company for that matter, to admit to a defect or flaw. The implications are immense.
This is exactly what I experienced with my upgrade. Was the worst upgrade I have seen out of DJI in over 4 years. No messaging around what was not going right with the upgrade. Completed upgrade and got the "Cannot Take off" message. The first upgrade did not upgrade the battery, did the refresh and away it went. But to your point, each battery had to be place into the Spark and updated , so it was like updating the aircraft 3 times, once for each battery I had. You really like to understand what was wrong with the firmware. Concerns me that the software quality might be lacking on the Spark.