I've just updated our OTRS from 6.0.0rc1 to 6.0.5 and followed these official instructions.
Mostly everything went fine except that we had previously disabled a few menu options from the Main Menu. We had previously only kept the "Dashboard" and "Ticket" dropdown visible for agents. These settings were disabled on Frontend->Agent->ModuleRegistration->MainMenu.
After the upgrade, all these settings appeared to be active once again. And also, when trying to disable them, we'd get a "This field is mandatory" on each of the "description" fields we wanted to set as disabled, so we had to fill out a dummy description in order to be able to bypass the validation error.
So, I guess my question is: is it normal for some of our sysconfig settings be reset when upgrading between versions?
Also, I'm not sure if anybody here has any access or control over the documentation. But the upgrade documentation should also remind users to restore any custom skins and template folders (on var/httpd/htdocs/skins and Kernel/Output/HTML/Templates respectively).