We, and several others, are seeing major performance issues on El Capitan 10.11.6 after installing Security Update 2016-003 (OS build 15G1212).
The issue is with Window Server going "out to lunch" after some period of uptime.
Separately, Apple has released i OS 9.3.2 update, watch OS 2.2.1, tv OS 9.2.1, and i Tunes 12.4.
If the user must reboot they need assistance from IT in order to get logged back in, and sometimes they need to reboot outside of official support hours.
The best way to ensure a smooth transition from an older operating system to High Sierra is with Time Machine.
If you don't already have a backup plan in place, there are a few options you can check out.
If anyone is seeing this in their environment, and has Apple Care, please open a case and reference the one above.
We have scientists and developers working with large data sets and having to reboot in the middle of work is problematic.