You need to "undo" (see "Edit" -> "Undo") the tree map layout result to revert the node size changes.
The state information that is necessary for that undo operation is only available while yEd is running. Once you quit the program that information is lost. I.e. if you save the result and quit, then start yEd again and open the saved result, you have to manually change the nodes to the right sizes.