Having read the comments about 3rd party batteries, I switched to the Canon battery before doing the firmware update.
When I put the Pearstone battery in I did get the screen saying: "Communication with this LP-E6 battery is irregular. Continue to use this battery?"
After answering yes, the camera went on to operate normally. The battery levels and charge capabilities are functioning and unchanged from before the firmware update. I only get the Communication screen one time after putting in the Pearstone battery, further camera restarts do not bring up the Communication screen. Removing and replacing the Pearstone battery does bring up the Communication screen, but again, only one time. So it appears that there are some chip differences among 3rd party LP-E6 compatible batteries. (BTW the Pearstone came from B&H)
After the completing the firmware update all my previous custom settings were still in place and unchanged including all my microfocus adjustments.