Chance of pw hash corruption and encrypted drive

I'm putting together a new Linux machine and am weighing the issues with encrypting the disks. I once had an Ubuntu box where the root password stopped working, so I had to reboot into a recovery shell to change the password. This wouldn't be possible with an encrypted drive. Am I just being paranoid? Did I just have an extremely unlikely experience? I'll be using Centos,not Ubuntu.

Also, are there safe alternatives to encrypting the entire disk/partition? Like if I wanted to encrypt folders that might have passwords in them like /etc and /home?

Thanks.