It was going to suggest splitting it but then i reread and saw you did that anyway. But maybe instead of having a file for each icon and add them to the map one by one, make a file that is the same size as the map image and place all the icons in their correct places on that, then you save that as a png whenever you make a change and when you add it to your map you dont have to place the icons everytime.
Although im not too familiar with photoshop method so there might be a better way to do it. But that is the best i can think off.
Or you could just not edit your icons again.