Imac shut down

[Rod]

So you may already have worked this out but what I would do is;
Boot from the clone,
Use Disc Utility to erase the internal drive at the media level (Samsung SSD 840...)
Now you can either download the macOS installer (my preference) use that to install a new copy of the OS then boot from it and use drag & drop from the clone to put back your data. You could also use Migration assistant to automate the process.
Using a macOS installer on a blank internal drive will ensure the file structure is correct.

Or, you could just reverse clone the EHD back to the internal drive but you run the risk of reinstalling any errors from the original drive.

Using the first method is essentially called a "clean" install which I used to do every couple of years. It doesn't take all that long to drag multiple files and standalone apps across to the internal. I usually re-download bigger apps.
You end up with more storage and a quicker snappier device.

 

[MacInWin]

Before you erase the internal, boot from the clone and run Disk Utility First Aid on the offending container/volume. It may be able to repair them for you, which will save the erase/restore pains.

 

[Steve_G]

Before you erase the internal, boot from the clone and run Disk Disk Utility First AidFirst Aid on the offending container/volume. It may be able to repair them for you, which will save the erase/restore pains.

First thought, why not try Disk Utility First Aid on the "CCC clone" disk. Did that and it was able to unmount the disk and repaired Disk. Except the Disk Disk Utility window froze, was not responding. Opened up Activity Monitor and "quit" on the Disk Disk Utility. Back to normal.

Rebooted with the option key and selected the CCC clone. Took awhile to come up, as I was going for the Disk Disk Utility icon, the computer shut down, Black screen. Had to pull the electrical plug to get it to reboot.

Ran the first aid on the Macintosh SSD, repaired successfully, no errors. I guess I'm "out of the woods"?