OR... they made note of him bringing it in jailbroken, and now even if he restores they have him flagged in that store (I don't think they have a nationwide store-to-store system yet, but I'll ask).
They can (and will) make it a point to punish those who bring in a jailbroken phone as it technically voids the warranty (i.e. they don't say "it's only void if you don't restore it before bringing it in").
While it's true you can hide your tracks, if you were dumb enough to bring a jailbroken phone in for work they have more than enough ability to make note of it just in case you try to cover your tracks later...