Out of curiosity, was it before you formatted the SD as internal that it used to work?
I ask because I've seen other people report that they formatted the card as internal and then could only see the card over a USB connection and not the true internal storage. As my phone doesn't have an SD slot, my tablet is running Android 5.1, and I've anyway no desire to format a card as internal, I cannot test this myself or investigate why, but it is something I've read before.
You are sure that it's not showing any of the internal directories, i.e. it's not just showing both stores as a single volume and labelling it SD? Otherwise unless someone knows an answer I'd start looking at workarounds, e.g. whether something like WiFi File Explorer or Airdroid can be used to back up over WiFi, or whether a flash drive and a USB OTG adapter could be used to do the backup from the phone itself.
(Of course if the update is an over the air one, the risk of data loss is very small. Different if you are manually reflashing the phone).