Edge Case where BACKUP=1 is missing
In this ticket https://admin.dimenoc.com/desk/ticket/2558811#note_3820925 there was an issue with two accounts missing after the upgrade. I found that the users had LEGACY_BACKUPS=1 in their /var/cpanel/users/$USER config, but BACKUP=1 was missing completely.
The check script currently only looks for ^BACKUP entries and missed this.