This process works with a healthy ST16. Your ST16 has some unknown issues. Please understand there is some risk to using this process for your controller.
1.) Ensure controller Battery fully charged.
2.) Format an SD card.
3.) Download "ST16_V3.1.30.yuneec" to the SD Card.
4.) Properly eject the SD card from your computer.
5.) Ensure ST16 is OFF.
6.) Insert SD card in the ST16.
7.) Start the ST16. and allow it to fully boot.
8.) Go to the Firmware update page.
9.) Initiate CONTOLLER update only (The top update button.)
Leave the controller alone for awhile. It will take time to unpack and install the update. The controller will reboot by itself at least two times. When the controller displays the normal main screen, the update is complete.
When the update is complete, you will need to go into settings, and clear any app data from the flightlog app. (Let us know if you need any details for how to do that.)
When the app data is cleared, you will need to set up the controller again, including making a new model and binding again.