Her dedicated server is a bit odd in it's setup and still doesn't give total control, so it seems to have the limitations of a shared host. Like the only shared account on the server.
Jane, if the user table corrupted or certain things were deleted from the database with a query, then JOINs would fail and various things can stop appearing. They may still be in the database, but simply won't appear.
For example, if you delete user #42 with a MySQL Query (or it gets deleted by corruption in the Database) then if they held the last post in any forums, those forums would disappear from the main index, and any threads they participated in would also not appear.
The missing user ids would either need to be replaced, or the IDs for that user in the various other tables would need to be changed to the #1 placeholder user.