@ Bec a Fuel - Sure you can connect them if you want but you are doing so at your own risk. The official answer is still these pins are reserved. Please do not connect them. We have not tested them and we do not know what the outcome may be.
I think there is a little confusion here Gus.
I don’t need to use them on the G400 for new designs. The issue is that I designed PCB a few years ago that used the ChipworkX and the WKUP pin was pulled to GND as per the specs. In my case, I grounded the pin instead of a pullup resistor on it. The designed without perfectly and there is a number of units still out there working away without any issues.
Then you discontinued the ChipworkX module and brought in the G400-D which was stated as being compatible with the ChipworkX electrically but we knew software would need to be changed of course.
Now the issue for me is the WKUP pin and what I need to know since this thread started is what are the consequences of this line being connected on the existing boards and is there a long term issue in doing so? You’ve said in your last posting that you don’t know what that is as untested. Eeek. I guess I will eventually find out. From the OP posting I would guess the battery drain is the main one. 
@ Dave McLaughlin - I understand and this is why we can chat privately about this. But the simple answer for everyone else reading this, follow the datasheet 
@ Gus Is there any chance to have those pins working in the future? Being able to wake up the design by pressing a push button is a must have of all modern embedded devices. Such a feature could be very interesting if it is a built-in feature of the SOM.
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We have looked into them long time ago and they did not work as expected. We can revisit in the future but we are now busy with other things.
Hey guys. We have resolved the shutdown controller problem. At a time when we had no idea where the problem was, the system sometimes did not wake up, occasionally could not wake up the WKUP signal, and occasionally the RTC was set to a value from a distant past. After three months we came up with a simple solution, made the shutdown controller work, and eliminated all the problems described above. See SAM9X35 documentation for solution 
We solved the sequence of starting the voltages 3.3V 1.8V and 1V. The problem was, however, in shutting down. The SHDW signal must pull NRST to zero and the shutdown controller will start working correctly.
GHI guys, we plan to use the G400S for commercial purposes (500-2000 pieces). Can we rely on WKUP and SHDN pins to be retained in the G400S even if you have omitted them in the new documentation?
Please contact us immediately and discuss your application. I have a feeling you are not on the insider list. You can ask for myself or @Greg_Norris