There's a 27-page thread on the Lenovo forum about charging problems with the Yoga 3:
https://forums.lenovo.com/t5/Lenovo-Yoga-Series-Notebooks/Yoga-3-Pro-Battery-Charging-Problems/td-p/2055358
I note that several people on that thread have thanked the contributor who posted the following, as it solved their own problems:
"I had the same problem and solved it by enabling "Battery Sleep Mode" in OneKey Optimizer. When you open OneKey Optimizer, click on "Save Power", then "Battery Conservation" and turn on "Battery Sleep Mode", then shut down your computer, insert the charger and turn it on."
Worth a try, perhaps?