Board Thread:Theories and Speculation/@comment-890307-20161205161301/@comment-30426414-20161219041638

Ravenlot 27 wrote: Well, what really matters is the fact the eyes are cured from the blindness, not how they are cured. Itachi impicilty said that Izuna's MS got an eternal light when its ownership was changed to Madara, thus becoming a more powerful doujutsu known as EMS, all thanks to this exchange. Moreover, I think that the interaction between the chakra of the original MS user preserved in the transplanted eyes and the chakra of the new owner results in the eyes themselves getting stronger than they were before, which includes the ocular powers getting a powerup and the elimination of the blindness drawback. Even if some merging process exists, it happents between the different chakra types within the transplanted eys, not literelly between two different sets of eyes.

That still isn't conclusive evidence to suggest the mangekyo are swapped. To me it makes much more sense that the transplanted eyes are merged with the originals because there are less assumptions regarding the reason why the eye patterns are merged and why the transplantee retains the abilities of the transplanted eyes.