I can see a way to reconcile the different versions:
-Nubia is a reincarnated princess from the Well of Souls.
-She becomes the guardian of Doom's Doorway and the first champion. She is also a nanny or big sister figure to Diana.
-One day there is a breach in Doom's Doorway and she is believed to have died.
-However, she didn't die but was lost and was teleported to the tribe on the floating fortress. She is amnesiac but still remembers how to fight.
-Later, either Ares or Phobos/Demios (Eris or Enyo could work as well) tells her the twin sister origin and manipulates her with a ring as a weapon against the Amazons.
-Nubia fights Diana who manages to undo her brainwashing and make her realize her true origin.
-Nubia reconnects with her Themysciran sister but her time away from them has caused some distance between the two. Eventually, once Hippolyta abandons the role of Queen, she defeats the odds and becomes Queen.