I have absolutely no idea how the "new setup" looks because it is too convoluted to determine where the various connections are. A dishwasher without a PROPERLY installed air gap CAN siphon the water out of the tub, whether it does or not depends on the timing of the fill cycle compared to the drain phase. The only possible damage would be to the heater if it was operating without water around it. IF the water siphons out, it CANNOT clean because there is no water to do it. AND, if the hose goes from the DW directly into the hole in the floor, the water will usually drain out as fast as it is entering the DW. The air gap, if you install one MUST go on top of the cabinet, not in the basement or anywhere else.