Either the manual’s out of date or you’re looking at a manual that doesn’t apply to Dorico 3 - I confess I haven’t checked whether the Dorico 3 manual’s been updated on this point.
The easiest way around this is to:
a. close Dorico
b. navigate to %appdata%\Steinberg\Dorico 3 and delete the preferences.xml file
The downside to this method is that you’ll lose all your Dorico application preferences (anything found in the main Preferences dialog, but not things like Layout Options/Notation Options/Engraving Options/Playback Options).
The slightly more tricky route that lets you hang on to your other preferences is
a. close Dorico
b. navigate %appdata%\Steinberg\Dorico 3 and open preferences.xml in a decent text editor (I recommend Notepad++ on Windows; it’s free and it works fine)
c. edit the line in the middle of this screenshot (line 136 in my case) so that the path is correctly set for your new user account (sorry; this screenshot was done on a mac)
The history to the option disappearing from Preferences > Files > Auto-save is this:
The Dorico Autosave folder is automatically wiped every time you close Dorico or a Dorico project via usual methods. If Dorico crashes or hangs, and you Force Quit or End the Process/Task, the contents of the Autosave folder is left intact (and the next time you launch Dorico you’ll be presented with a list of Autosaved projects for recovery). When the Autosave function was introduced, some users failed to understand that the Autosave folder would regularly be automatically wiped, and set the AutoSave path to their Desktop, or their Dorico Projects folder, or their Documents folder. They then complained when Dorico automatically deleted everything from their Desktop/Dorico Projects folder/Documents folder. For this reason, the Autosave path has been removed from the Dorico Preferences folder. Really, the only downside to this is the scenario you’re in right now.