CrashPlan supports backing up encrypted files, folders, drives, and filesystems that run at a system or user level.
FileVault 2 is compatible with both of the CrashPlan app's installation options: installed for everyone (default), or installer per user.
There is an option in Truecrypt enabled by default called preserve timestamps of file containers. When enabled, Truecrypt retains the file timestamp from initial file creation. Essentially, it looks like the file has never changed and the CrashPlan app won't back up the changes. If you disable this option, the file timestamp changes when files are modified, which allows the CrashPlan app to back up the changes.
BitLocker drive encryption
Windows BitLocker Drive Encryption provides full drive encryption. Since BitLocker runs at a drive level, the CrashPlan app is able to back up drives protected by BitLocker when the drive is in an open or unlocked state (decrypted at the drive level).
However, when the drive is locked (encrypted), the CrashPlan app can't back up the files and may report the drive as missing. If the CrashPlan app reports the drive as missing when it is unlocked, you may need to run a file verification scan.
Because the CrashPlan app backs up your files when they are unencrypted, they can only be downloaded as unencrypted files. You can download these files on other devices or using the CrashPlan console without worrying that the files will download in an encrypted state.
Windows Encrypting File System (EFS)
Windows EFS runs as a user. Consequently, the CrashPlan app must be installed per user to back up files protected by Windows EFS.