The short answer is yes, you would still be in a hypercube.
How can you verify this? Well, the only way you can ever verify anything about the fourth dimension... by using analogies with other dimensions. Imagine now that you were a $2D$ creature walking around on a cube.

As you can see, you would have only four directions in this case, and there would be only $6$ rooms.
The problem is, you can't really make a graph with "directions" labelling each edge, because your orientation is constantly changing. For example, if our quadrilateral friend travelled North and then East from there, he would end up in the same place as if he had just travelled East... but he would be facing in different directions when he arrived.


So when you're a being messing around in a solid of a higher dimension, it doesn't make sense to think about "directions" anymore. For this reason, your graph isn't accurate, because it is static - in reality, the "direction" in which you would travel from one room to the other would constantly change, and so the labelling of the edges would constantly change. Thus, if you made the swap of labelling that you are asking about, you would still be in the same solid - in fact, you could probably achieve that very orientation just by walking around for a little bit inside of it.
e.g. interacting inside the 3d cube rooms, is really just the 'surface' of the hypercube.
– Ryan Leach Jul 07 '17 at 15:52