Maybe a litte late for you, but Yunnec Europe postet this on facebook:
1. Download Software V1.28. You need this Software as a basis to start updating again. Download here: http://files.yuneec.de/TyphoonH-FC_V1.28_24_9_2016.yuneec
2. Open Typhoon H GUI Software.
3. Go to „Tools“ slide above. Then „Firmware Update“.
4. A pop up window shows up. Go to „…“ and select the Software Version 1.28 file.
5. Remove battery from your Typhoon H. Connect USB cable to copter and laptop or PC.
6. System starts to update your Typhoon H. Wait until it was uploaded correctly. Close program.
7. Remove USB cable. Insert battery.
8. Upload newest software version 3.0 to SD card. Insert SD card into the CGO3+.
9. Turn on ST16 and Typhoon H. Wait until you can see the live image of the camera on your ST16.
10. Go to „System Settings“ on your ST16. Then tap "About Controller“.
11. Click „Update“ for Typhoon H and the system should start to update everything to the newest version.
12. For checking go back and then again go to „System Settings“ —> „About Controller“.
Yes it's a bit confusing that the GUI requires you to load the firmware first and then connect the H (powered down).