To update a dual-booted or rooter Gemini, you can do 3 things, one of which made possible by me having done one of these.
1. Wait for Planet Computers to release the new firmware and only flash the system.img.
2. For dual-booted Gemini: Back up everything (instructions on Github wiki), flash fresh non-rooted firmware and install update official way. Then back up again and only select system.img in WWR tool.
For rooted Gemini: flash back unrooted boot.img, update official way, then install rooted boot.img again. (I have not done or tested this method.)
3. Download and flash my system.img that I made with step 2. You can download it here:
https://drive.google.com/folderview?id=1q_H...DZvOHYHBcWZQx0CI did step 2. It costs some time but works perfectly.
I'm not responsible for anything you do with this information however.