I talked to the bee guy, he said only things he could think of is they are using something called bt or tb on the corn and bean crops to make the insects not like the pollen, but from what he understood, it did not hurt them, just made them not like it. Also the only other thing is if the honey gets old it will ferment and that could affect the flies. One more note, if the honey gets old, on top of the fermenting, it can get some parasites in it to, he said to change it frequently to keep it clean and not to use old honey, he said very unlikely to have something bad in the honey, but not impossible.One of the most interesting posts yet, Rebecca. Biotech BT corn and cotton are modified to repel insects like weevils by producing bacteria. You can find plenty of documentation for and against its use, particularly in regards to bees, but Australia has been using this for years and doesn't have CCD. No one, though, has even suggested that this bacterium lives on in the honey.
Personally, I have never seen honey so old that it had started fermenting, and I image that it would be visible and sniffable if it did.