All I can tell you is what I'm observing from your now 3d color flower drawing vs your original Source dwg.
They both have a total of not 4294 cubes as you stated but actually only 3792 cubes as I've stated.
The 3d color flower drawing shows one of those objects with your 5x5x5 cube in the center and then surrounded with a number of other objects that makes up a much larger object but still it's classified as a single 3D Solid:

The source drawing shows your 5x5x5 cube again as a 3D Solid object but only at 5x5x5 without any of the surrounding geometry:

At first I thought the use of the MeshSmooth command is the answer. But that changes the object to a Mesh and no longer keeps it as a 3D Solid. On top of that it doesn't add any other geometry around the object to make it any larger in size:

So I'm at a loss as what single command you may have executed that would have given you from a 5x5x5 source 3D Solid to the now much larger 3D Solid object.