Dave, thank you !

Time machine may grow as it is on a separate partition and f the partition is 'full', old TM entrees are sill deleted right ?

For safety reason I might be better to erase the SD clone partition only; than is the TM partition still there :)

Yes, old TM data will then get deleted, but that won't help the other volume which is now full. So, I'd keep the TM volume HFS+ and add the APFS volume as I described.

It worked, but the 2nd drive isn't actually bootable...
 

I tried this on two separate external drives that used to be bootable after a SuperDuper clone prior to high sierra. With the beta and APFS, while SuperDuper does complete the copy process without any errors now, the cloned drives neither appear in the "System Preferences - Startup Disk" options, nor they appear when rebooting the macbook and pressing the "Option" key to select a boot disk.

As an FYI all my drives are encrypted with FileVault - never been an issue before APFS.

Side story - went to Apple Genius bar to repair my macbook - their hardware tests in the store now fail to run if using High Sierra as they do not see boot disks as they are all APFS volumes now...

So, one drive worked and one drive didn't? (You said '2nd drive"....)

Did you format the backup drive as encrypted? Or did you encrypt by starting up from the backup, THEN turning on encryption and booting back?

The Beta worked for me!
 

Thanks, Dave...All all went well after following your patient instructions. One partition on my external non-SSD drive now contains an APFS clone of the 240GB SSD; the other partitions, including Time Machine, remain as HFS+. (SuperDuper! Time: 2:40:40)

Glad to hear it worked!

Sorry - the title was misleading. here is the scenario.

My Macbook was running High Sierra with the boot drive having been converted to APFS during the upgrade process (drive is encrypted via FileVault).

I then formatted two external USB drives with APFS (encrypted). Run SuperDuper 3 to duplicate the boot drive onto the both USB drives. No problems during the copy. I did on two disks just to be safe - I had to bring the macbook for repair so wanted to have two additional backups in addition to TimeMachine.

I then discovered that neither of the two external USB drives were bootable. Connecting them to another macbook showed the USB disks just fine when the macbook booted up, it's just that they were not bootable.

Semi-good news though. I ran the Disk Utility on one of them and selected the repair option. The Disk Utility didn't report any issues... but when it was done the USB drive now appeared as an option in the Startup Disk in the System Preferences, and I was in the end actually able to boot from it.

But now I'm discovering other problems... when booting from the SuperDuper-made USB drive that got fixed, not everything was copied correctly. For example all the extensions in Chrome have disappeared, and some of the plugins in Safari are also gone. So far those are the only problems that I see after using the USB drive as a boot disk.

The 2nd USB drive that I had SuperDuper'd is still untouched (not fixed by Disk Utility yet) as I want to keep it intact just in case I find other issues with the 1st USB drive that was cloned.

Interesting. The missing extensions seem quite unusual. Can you send me a support email? That's going to require more extensive investigation, since I'm not seeing that here.

Sure - I just sent you an email to your feedback email address. It said (also in case others have similar issues):

======================

Hi,

This is ik8sqi from the forum with the High Sierra / Safari/Chrome extensions issues.

For Safari so far I've compared the directory on the USB drive:
/Users/cmctrf1/Library/Safari/Extensions

with the same one in Time Machine, and except for the "Extensions.plist" the files where the same.

For Chrome instead, the USB drive's directory:
/Users/cmctrf1/Library/Application\ Support/Google/Chrome/Default/Extensions

contained only a couple of random folder names, while the one on Time Machine contained 13 such folder names.

In either case (Safari/Chrome), copying those folders from time machine onto the corresponding filders on the USB drive did not solve the issue - the extensions where still missing in both Safari and Chrome, so some other files are not being copied correctly.

Unfortunately I do not have my original computer as it's now being repaired by Apple. All I have is TimeMachine and the two backups made by SuperDuper...

Roberto