-If this is FOSS or NE without ZCO, those contacts were probably local to his system (I assume your not showing any in address books in the account on the server).
-I highly suggest IMAP instead of POP if you can afford to store the mail on the server. Unless they select 'leave a copy on the server' or you duplicate it to a
user.archive@domain.com, backups become the user's responsibility - and we all know how that'll end up.