Some day I am going to have to do an experiment. Take a small sample of honey and leave it open at room temperature, and a comparison sample in the hive, but with a way to keep bees out. Then every week, take a sample and test with my refractometer.
I don't think swabs and cultures would really help, as the culture medium is not a true reflection of what is happening in the honey. If I was going to set up a test for this, I would take a sample and make a smear on a microscope slide, staining it for yeast, bacteria and bacterial spores (C. botulinum etc). Might need to do it by taking a known volume of honey, diluting it, spinning the bugs down, then smearing the spun pellet onto a slide. It would be tedious, but if people are really worried, it might give an answer.
Having gone so far down this road, I now need to back track a little. I think bacteria are not very good at growing in hyperosmolar solutions (even under-ripe or diluted honey). Yeasts are much better at it. However, very few yeasts are pathogens, so even if they did multiply in the honey remnant, I can't think that it would be toxic or "infected", just slightly alcoholic.
I didn't get a Flow harvest this year, but I think I will probably rinse the frames in lukewarm water, in particular flushing the channel. The bees should take care of the cells next season - they won't store (or add to) fermenting honey.