Password protect
Encrypts the file itself, so it can't be opened in any reader without the password.
This produces a download, not a stored change.
An encrypted file can't be thumbnailed, searched or edited without the password, so the copy kept here stays unencrypted. Protection is a way of handing the file to someone else.
Going the other way — removing a password — happens at upload: drop a locked PDF in and you'll be asked for its password once, then it's stored unlocked.