Edit:
Apparently I fail at reading comprehension. On the firmware update page for X-E2 it says for upgrades from 1.00 to 4.00 to execute SET-UP > RESET > SHOOTING MENU RESET and SET-UP RESET. After doing that everything works and I am back in business. Hope this can help someone else.
Original post:
I just upgraded to 4.00 from today on my X-E2 and have a similar issue. @perspektive says it worked fine for ~100 shots, but mine failed right away. I also Googled solutions saying to upgrade the firmware again, use different cards, reformat the cards before and after the upgrade, and different batteries, but also no luck.
The first time I turn on the camera after the firmware upgrade:
1. The display only appears in the EVF, which is weird since I had set it to display in the LCD.
2. Taking a photo results in the rear LED to blink orange and green indefinitely
3. The UI is completely unresponsive at this point. I can no longer take new photos, change settings, go into menu, or interact in any way with the camera since I believe it's waiting for a disk write.
4. The on/off switch is also unresponsive. No way to turn off the camera except for ejecting the battery :-(
Any subsequent attempts to use the camera slightly differs in step 2:
1. The display only appears in the EVF, regardless of if I changed it in the last run.
2. Taking a photo no longer causes the rear LED to blink or to turn on at all.
3. UI is unresponsive again.
4. On/off switch also unresponsive. Eject battery :-(
This is definitely reproducible across my Transcend and SanDisk Extreme Pro SD cards, and my Fuji and third-party batteries.