http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1857359/) Bt toxins are not even broad based in their effects on insects. Due to the host-specific nature of a couple of the steps, Bt toxins only affect certain classes of insects, depending on the Bt species from which the toxin was isolated.
On top of all that, to produce HFCS, the corn kernels are subjected to high heat and strong acid in order to convert the starches into simple sugars. Both of those things are VERY hard on proteins, and tend to destroy them quite quickly. So, the chances of much protein even making it into the final HFCS product is pretty small.
As far as long term effects go, sure, anything is possible. But, the most likely effect would be the same as is in insect guts, and that is a VERY short term effect, which would be noticed quite quickly.
I deeply respect a lot of the writing you do and your experience as a beekeeper, but I think that in this case, the implication you make about Bt being present in HFCS and being able to do *anything* in a human digestive tract needs some evidence to back it up. Otherwise, it's pure hand-waving speculation.