1. The trouble started after I upgraded from Yosemite to El Cap. I use a conventional HDD in a Thunderbolt - USB 3 enclosure. I will (when I have some time) erase that clone and re-clone with CCC.
I just did this and the clone booted without incident. I ran some tasks with it and all seems well. However, CCC reported that it had lost connection with the clone when it offered to make a recovery partition. This didn't happen with the SSD clone made with CCC.