My entire point was that the Stokes theorem requires simply-connectednes to hold.
This is true, but the Stokes theorem is just mathematical transformation. Vector potential could still be used to describe the effect.
OK, I think I understand your question. You assume hypothetical world which has an infinite cylindrical hole inside which the field is B is nonzero, and worry whether the explanation of the B-A shift really works for such setup (because perhaps there is no vector potential). I believe the answer is no, but for a different reason.
First, I think it is not necessary for the standard quantum-theoretical explanation of the shift. One should get it for ordinary simply-connected space, otherwise there should not have been so much fuss about it.
But let's adopt the above assumption to see where the argument for the shift fails.
1) The toroidal space T we consider has zero magnetic field everywhere. The vector potential can be introduced, but in order to do that, we have to require some conditions. The obvious one is
<br />
\nabla\times\mathbf A = 0,<br />
but this is not sufficient, for there are more solutions to this equation. One of them is \mathbf A = 0 everywhere in T, which gives zero loop integral and no reason for the shift. So, in order to get some, we have to arrive at a different potential, like that which circles around the hole.
2) What is the reason for any definite choice different from A = 0? Besides the above equation, we have to impose another condition, and the only thing left are the boundary conditions in the infinity and at the inner radius.
Now, in ordinary physical space one uses Coulomb vector potential, which is nonzero and circling on the surface of the coil. If one takes this condition to the inner boundary of our space T, one gets the same vector potential and we have a reason to expect some shift.
Now assume the current in the coil is reversed; then the direction of the potential on the surface is opposite, and if we copy this again into our boundary of T, the predicted shift changes sign.
So, there is vector potential mathematically, but we have to copy the boundary conditions from the real situation where the coil is part of the system. For this reason, I think that the idea that the effect has something to do with breakdown of simple-connectedness is wrong.