Aside from my general narrative gripes with the decision to give Six amnesia, this introduces a major issue for the finale. Throughout "Endgame" Six recalls a promise he made to White Knight: if Rex ever turned into that monster again, he would put him down. Six seems to recall this more than White Knight, who says something akin to "whatever promise we made, disregard it." Unless Six somehow regained his memories, this plot thread makes no sense.
I don't know, this has just bugged me for the longest time. Why give Six amnesia if it never becomes relevant again?