WD My Passport has deleted an entire directory

I had to send my MacBook Pro away to be repaired. So I backed it up completely onto a 1TB WD My Passport. Then I plugged the WD My Passport into my MacBook Air to access some of the files that were on the MacBook Pro that I sent away for repairs. Today, I have discovered (to my consternation) that the entire backup of my MacBook Pro is gone! I’m guessing that WD Passport has overwritten it? Would this be correct? Is there anything I can do to restore the backup from my MacBook Pro?

You can scan your external hard drive with a data recovery software; however, if the files are overwritten then the software will not recover it. Are you sure? Still I would suggest you to download the demo version and scan your storage media. If some files are still not erased securely then you can recover them. Read more How to Recover Overwritten Files from Mac Drive?