Hey !
For what it add,I'd like to share my experience on this issue as well: I have the yoga 3 Pro since 2 years now, and I confirm I experience the same kind of issue.
Now, I am using Linux Ubuntu 16.04 as an OS, and the system does not freezes completely: only the touchpad gets out of sync. SO basically I can still use the touchscreen, the key board etc... The touchpad is completely frozen until complete reboot. If it were some firmware/driver/software problem, I guess some commands (particularly in Linux where we can access a bunch of commands to the heart of the system) would be able to relaunch the touchpad. So far, I tried quite all commands including Reboot. But the freeze is not "released" until complete shutdown + restart: this is the UNIQUE solution to get the touchpad live again...
That being said, I think total shutdown allows some static electricity from being completely released where other solutions can't discharge it (rebooting keeps the laptop under electrical tension). So my best guess is that this problem is pure hardware mess.
To illustrate further, I changed OS 5 times: windows 8.1, windows 10, Linux Mint 17, Linux Mint 18, then Linux Ubuntu 16... I experienced the problem with ALL OS....
As a log for anyone who sees this, `dmseg` command on Linux shows this message the second after touchpad freeze:
[ 2060.782668] i2c_designware INT3432:00: i2c_dw_handle_tx_abort: lost arbitration
[ 2061.786144] i2c_designware INT3432:00: controller timed out
where `i2c` basically refers to the touchpad, it explicitly says that it "lost arbitration".
Now given all previous comments, where I see some solutions advocating either driver updates and some of those things, I cannot say updates won't solve the problem either. In fact, what I think is that those updates work at preventing some conflicts between the original problem and the OS (like creating specific cases that would know the problem and send some commands to reload .dll or reload some sub-programs) to create the illusion that the problem is gone.
Finally, before reading this thread I thought I was alone and it was my fault because of preferring Linux over Windows or some dumb assumptions like this... But indeed, after some trials, I too am affected by the `don't touch the screen` problem.
So I believe the problem is more likely to be a hardware conflict with that cool functionality (we all felt in love with) that allows the screen to be flipped in several modes. Some sensors must have been stuffed into the hinges or something like that, and those could come to make interference noise together with the bluetooth/wifi card, leading to a rare conflict: then depending on the OS you are using, this panic translates into various weird behavior.
Even with this long post, I unfortunately don't have proper solution for now. For the record, I switched the Broadcom wifi card with the Intel one: same thing... I am left to try to maybe open the laptop again and reposition stuff around to see if something changes until I finally decide to throw this Lenovo crap to the trash bin !!
Cheers