Thanks for your helpful insight. I was booting from an external usb drive that is HFS+ formatted. Is there as way to fix the recovery partition problem or even check if there is one on the disc? I am testing the patcher with this clean install to see if I should update my main El Captian install and have current security patches. It makes me nervous about trusting a full system when each security update has glitches!
What exactly did you mean by Post Install. I am a bit rusty as I first put this drive together a year ago and have just come back to the project as I felt I really needed to get secure.
I meant what is the format of the drive you have High Sierra installed on, not what the installer drive is. And what I mean by post install are the kexts and other patches you need to run after install, and sometimes after updates. You'll see it in the bottom left of the interface when booted to the installer.
This is what I recommend:
1. Make a current Time Machine backup of your El Capitan drive.
2. Boot from the High Sierra installer, open disk utility, and format the drive you had El Cap on as "APFS".
3. Install High Sierra on the drive you just formatted.
4. Boot back into the installer when it's done and reboots.
5. Double click on "Post Install", then select your machine, then the drive you installed HS on. It will reboot when done.
6. Let the system boot normally into setup, then when you get to the restore data screen you just select the drive your El Cap backup is on, and restore that account into High Sierra.
The end result will get exactly what your El Cap install was, but on High Sierra.
When you install updates they should work without a hitch on an APFS drive, but with the more recent updates (like 007) you will also need to do the post install again from the installer.
Do exactly all that, and you'll be golden.
Also, if you don't have an El Cap installer drive then make one first. Just in case something goes south, which it likely won't, but you'll have the El Cap installer and backup in case you feel the need to go back.