no way to say for sure without looking at the equiptment. but I have seen it a few times before.
if in fact the coil was designed to be on the return side of your air handler, and was properly installed, then changing the air handler to a furnace of the proper size will not be a problem.
You might want to look into the possibility of adding a heat element into your air handler to save some money. many air handlers have the option of heat elements being installed directly into their cabinets with no sheet metal work involved.