Thanks fro reporting the same here.
Joboptions can be found in /Library/Application Support/Adobe/Adobe PDF/Settings not in /[username]/Library/Application Support/Adobe/Adobe PDF/Settings.
To access the same one needs to go to "/Library/" instead of "~/Library/"
I have tried both of those locations, see screenshots, all the presets are still there.
I have restarted Illustrator and my machine entirely and they are still there.
Are they not hiding somewhere in a config file of sorts? I think I might have read somewhere once that it might be?
Why has this been marked as solved when it most defnitely is not?
I unmarked the previous response as being correct.
His response was strictly for Acrobat.
It turns out that each application that exports/saves PDF has its own copy of the Standard joboptions in its own location
To find them all, you are probably best off running a search of your system disk's file system for Standard.joboptions and delete those that you really don't want to use. Note (1) that the files might be protected and require you to change permissions to be able to delete and/or move them and (2) it might be prudent to save a copy of these files if you decide you want to use them subsequently.
Further note that each time these applications are updated to a new version (and sometimes even for minor updates), a new copy of the Standard joboptions file may be installed, requiring you to remove or move them again.