Hi Jesse, you should have known something was utterly wrong when you couldn’t fill those Faces with F.
My wild guess is that you had accidentally hidden those Faces and had a situation something like this:

As you can see in the statistics, the Cube still has 6 Faces, but it looks like the top Face is missing, but when you try to fill that with F, nothing will happen!
What happened when you used SHIFT+H the second time, I don’t know, but probably another case of hiding the wrong things.
H and SHIFT+H don’t make things go away, they just hide things…