As far as I can tell, the apple claim refers to the ergodic hypothesis, which implies that each microstate of a system will be assumed over time. In the apple example, the macrostate is the box containing a given collection of atoms with a given energy. The apple being whole is one microstate and thus it will need to be assumed again by the ergodic hypothesis.
Now, the ergodic hypothesis is, well, only a hypothesis. It is impossible to empirically check as such, but we use it as the foundation of statistical mechanics, from which several empirically confirmed statements are derived. Also, all known toy systems that break the ergodic hypothesis are somewhat pathological and I see no reason to assume that the apple system is one of them.
If we assume true quantum randomness, we can see how the apple might become whole again: It is possible to find a chain of state transitions from every given state to the apple being whole: Atoms just need to collide with each other in a given way. This chain is admittedly very unlikely to happen, but the probability is not total zero. Thus if you wait long enough, it will eventually happen, though you cannot say when. (Mind that this doesn’t prove ergodicity as that would require showing that all states are equally likely.)
You might compare this to applying random transformations to a Rubik’s cube: Most of the time, you will get an unsolved cube, but there clearly is a chain of transformations that solves the cube from any given state¹. Thus if you apply random transformations long enough, you will obtain the solved cube. Also, all possible configurations of the cube are clearly equally likely, including the solved one. Mind that if you have a deterministic chain of transformations, it may not ever visit the solution, but a random one is bound to.
¹ I here assume that the cube has not been tampered with, e.g., by prying out an edge stone and flipping it.
Wouldn't the cycle would very likely be a cycle through a bunch of states of very high entropy?
The thing about entropy maximisation is that it is only a statistical statement, i.e., it only holds when looking at large ensembles of particles (or similar) and only with a probability that is sufficiently close to one to assume it to be true for all practical purposes.
The apple example destroys the underlying assumptions by waiting an infinite amount of time.