I'd recommend having only 1 map/map pack in your exports folder at a time, to avoid any conflicts that could occur do to overwriting files (especially if the maps try to modify the default objects.).
Another thing to be sure of is that you put all the exported map files in the FeralHeart/exports folder.
You could keep extra maps in a backup folder somewhere else on your PC like this "Maps/Map1+Map2+Map3", Where every name is a new folder with a different map or map pack.
Edited: Thanks Bloo.