You have to pull the cables at the battery and let it set if you want the soft reset. Apart from that I would highly recommend NOT updating firmware via the app. I have seen more than one Shimano Di2 system become inoperable from firmware updating via Bluetooth/app.
With 12spd unfortunately you're going to be best off finding a shop with a PCE02 diagnostic tool to push all of the firmware updates and do testing and find any error codes if the soft reset doesn't work.