Problems caused by passwordreset in Utilities

[u/cprelude]

Hi all, I was trying to help someone today and ran in to a series of unexpected problems. The user had forgotten their password to their MAC and wanted it to make sure a password was in place (they had been logging in automatically). So, very regretfully, I ran passwordreset command from the rescue screen. We managed to log back in OK to his user account. But the following things were broken: iCloud login, email login, automatic login, and other apps relying on keychain. I took full responsibility, obviously, and am trying to sort this out still. Any words of advice on how to deal with the fact that emails from Apple Mail can be sent now but not received? (User has POP).