Carbon Copy Cloner offers complete support for archiving, cloning, and recreating Apple's Recovery HD partition. See the Cloning Apple's Recovery HD partition section of CCC's Disk Center documentation for instructions to create a Recovery HD volume on your backup disk.
When do I need to create a Recovery HD volume?
CCC bootable backups offer similar functionality to the Recovery HD volume, so the Recovery HD volume is not strictly required on a backup volume. Unless you have a specific reason to not create a Recovery HD, though (e.g. because it could affect a Boot Camp partition on the same disk, you don't want to give up the 1GB, etc), we recommend that you maintain a Recovery HD volume on your backup disk. Especially if you intend to use your destination volume in production (e.g. you are migrating to a larger disk, or restoring to a replacement disk), or if you intend to enable encryption on the backup volume, then you should create a Recovery HD volume for the destination volume. If you intend to enable encryption on the destination volume, we recommend that you create the Recovery HD volume before enabling encryption. A Recovery HD volume is not required for restoring an installation of macOS from a CCC bootable backup.
What is the difference between archiving the Recovery HD and creating a new Recovery HD?
During the course of an ordinary backup of a volume that contains macOS, CCC will automatically create an archive of the Recovery HD associated with that volume. This archive is stored on the source volume, and is subsequently backed up to the backup volume along with everything else. This archive of the Recovery HD volume can be used in the future to create a new Recovery HD, and it's the first source that CCC considers when you choose to create a Recovery HD. The archive is not, however, an operational Recovery HD volume, it's just a backup file.
CCC's Disk Center offers the ability to create an operational Recovery HD volume as well. This functionality is completely separate from creating an archive of the Recovery HD. Unlike the archiving of the source Recovery HD, creating a new Recovery HD is not something that happens automatically, you have to ask CCC to do this in the Disk Center. When CCC creates a new Recovery HD, it borrows space from your destination volume to create a new, hidden volume on that disk. The resulting Recovery HD is fully operational — you can boot your Mac from it and reinstall macOS. Refer to the previous section to determine if creating a Recovery HD is required in your situation.
Why were other volumes on my disk unmounted when I created a Recovery HD?
CCC uses a command-line version of Disk Utility to resize the donor volume. Resizing that volume requires making changes to the partition table on the disk, and Disk Utility may choose to unmount other volumes on the disk while it makes those changes. CCC will specifically remount the donor volume, but whether Disk Utility remounts the other volumes is a function (or bug) of Disk Utility. You can remount these volumes manually in Disk Utility.
Can I configure CCC to not automatically archive the Recovery HD onto my source volume?
Yes. Click the "Preferences" button in CCC's toolbar and uncheck the box next to "Create an archive of Apple's Recovery HD volume".
No, not with CCC. Creating a Recovery HD requires borrowing space from a physical volume, and that is not a modification that we recommend making to an underlying member of an Apple Core Storage logical volume. The only Apple-supported method of creating a Fusion volume is via Disk Utility or the macOS Installer, and each of those will create a Recovery HD volume before the Fusion volume is created. If you intend to create your own Fusion volume using one of the various tutorials available on the Internet, and if you want that volume to have an associated Recovery HD volume, we strongly recommend that you create a Recovery HD volume before creating the Fusion volume. You can use CCC to create the Recovery HD volume on the slowest disk that you intend to add to the Fusion logical volume group. See the following document for a demonstration.