What do you use?
For backing up and recovering files, I just use a simple COPY command: cp -av source target
This recurses and copies everything from the base source directory on down. It also preserves all file ownership and permissions.
It works fine whether or not the data is encrypted.
If you're copying information outside the file system (eg, disk drive formatting info), then use dd: dd if=device_name of=device_name some-parms-here
My understanding is that Clonezilla does the same thing as DD but is more intelligent because it only copies blocks containing data (not all blocks). So it's usually faster than DD... sometimes much faster. Plus it has a nice interface. And it's smart enough to employ different underlying copy tools depending on the partition type.
As you know, Clonezilla is in fact a full bootable linux OS bundled with its own special-purpose interface and copy tools. I've used it over the years for partition and disk drive imaging and have never had any problem with it. But for simple data backups, I still just use the COPY command because this works from inside the current OS and does not require booting Clonezilla.