Situation: new MacBook with OSX Sierra. Set up with an admin account, enable FileVault (taking note of recovery key obviously!) and install the necessary. Create account for end user and give it to them. All is well (after getting some USB-A to USB-C converters…)
User restores all his stuff from a Time Machine backup to the account on the new system – this overwrites all the current user settings. After rebooting the system, his account has disappeared from the login screen.
Solution: Log on as the other administrative user (luckily we have one!) and open the Settings – Security & Privacy – FileVault. A notice at the bottom of the dialog box appears informing you that there are some users that are not enabled to use FileVault, with a button to enable the users. This brings up a list showing the missing user. To enable the user their password needs to be entered.