That corruption with APFS is scary. I just made my second backup on an 8TB external with all my files. Could it possibly be due to how much you allowed and actually used in the volumes? My volumes are all in one APFS container, and I set the parameters so that the maximums do not go beyond the limit of the actual space. My only guess is that there was a problem with volumes trying to consume more drive that you had. That might account for all the drives showing corruption. Just a guess as none of us know very much about APFS, as Apple looks like it isn't sharing the limits of its new file system. but I also have old HDDs which are full of SuperDuper clones that I access through a dual disk dock that accept either 2.5 or 3.5" SATA drives. I've had this system for years so it is HFS+. I know I have run into several problems with Super Duper, but all the problems have been solved without loss. Perhaps there are problems with CCC? I doubt it, but make sure you have the latest version as my SD version has changed several times in the last 6 months or so.