Drawback of Multi Level Encryption

I am backing up my files to a RAID mirrored HDD, that has full disk encryption (FDE) in place with LUKS. Until now I did this with rsync, but I recently switched to a new backup program that does file level encryption as well.

So my question is: Is there any drawback of having multi levels of encryption, or is it actually an advantage? A drawback I can maybe think of would be managing two keys and forgetting one of them would potentially make my backup completely useless.