I uploaded a copy of a world to realms that had used a lot of the nether as a travel mechanism. In realms previous work in the nether did not carry through. I suspect that the end will also be missing on our realm however I have no way of checking this.

Have tried several different world uploads to my realms account, on every occasion neither the nether or the end is uploaded to realms, only the overworld, this includes back ups which have been downloaded from realms and then re-uploaded.