To my understanding 4.6.0 just added Korean language, otherwise it is the same as 4.5.1 which made the drive connect smoother. I.e. there is no real need to update to 4.6.0.
On the other hand if Shimano follows standard versioning schemes, 4.6.0 should add more than just a language module for...
Next time you should disable wifi while updating. Some phones use same chip for all radios and if there is a lots of wifi-traffic and/or poor reception, it might affect also BT.
There has been several reported cases in Finland where update over the air has bricked the bike. Sometimes it just...