CCC is fully qualified for use with FileVault-protected volumes (HFS+ and APFS). CCC offers some advice around enabling encryption in the Disk Center.
If your goal is to create a bootable, encrypted backup, use the following procedure:
- Follow CCC's documentation to properly format the destination volume. Do not format the volume as encrypted. Choose APFS if your Mac is a T2 Mac (e.g. iMacPro, 2018 MacBookPro; see the full list here).
- Use CCC to back up your startup disk to the unencrypted destination volume.
- Click on the destination volume in CCC's Disk Center, then click the Recovery HD button to create a Recovery HD volume. Note: You must be logged in to an administrator account to perform this step. [This step is unnecessary if your destination is an APFS-formatted volume]
- Open the Startup Disk preference pane and restart your Mac from backup volume.
- Enable FileVault encryption in the Security & Privacy preference pane of the System Preferences application.
- Reboot your Mac (it will reboot from the backup volume).
- Open the Startup Disk preference pane and restart your Mac from your production startup volume.
- Configure CCC for regular backups to your encrypted backup volume.
Additionally, you do not have to keep your Mac booted from the backup disk for the conversion process to complete. You can simply enable FileVault encryption, then immediately reboot from your primary startup disk and the conversion process will carry on in the background. Encryption will continue as long as the backup disk is attached. macOS doesn't offer a convenient method to see conversion progress, but you can type diskutil apfs list (or diskutil cs list if the applicable volume is HFS+ formatted) in the Terminal application to see conversion progress. Some users have found that conversion may not resume until you log in to an admin account while booted from your production startup volume, so try that if conversion appears to be stalled.
Enabling FileVault on the destination means that the volume starts out unencrypted, and then over the course of several hours the data is encrypted in place. If the encryption conversion process completes successfully, then for most intents and purposes, no trace of the unencrypted data will be left on that disk. There are some caveats however. If your backup volume is an SSD, and if you delete files from the SSD prior to enabling encryption, then the SSD may automatically move the not-yet-encrypted underlying blocks out of rotation (for wear leveling), and those data could be recoverable by experts. Likewise, if the conversion process fails for any reason, then the data on that disk is potentially recoverable. If either of these scenarios is not acceptable, then we recommend that you exclude any sensitive data from the initial backup task. Don't exclude your whole home folder — you must include at least one folder from your home directory so that you can log in to that account on the backup.
After you have booted from the backup volume and enabled FileVault, you can then reboot from the production startup disk, remove the exclusions from your backup task, then run the backup task again to copy the remainder of your data. Any data that is copied to a volume that is in the midst of encryption conversion will be encrypted immediately.
If your backup volume won't be a bootable backup of macOS, simply right-click on that volume in the Finder and choose the option to encrypt the volume. If your Mac is running macOS High Sierra or later, please note that macOS will convert an HFS+ formatted volume to APFS when you enable encryption in this manner.