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The manga originally implied that the 2 pairs of eyes become one permanent pair of EMS, hence the combined pattern.
However, in Sasuke's case, their is strong evidence pointing to the possibility that he simply had Itachi's eyes transferred and his old ones were discarded. Not to mention Itachi's whole plan with Naruto's gift revolved around Sasuke taking his eyes and the Jutsu reacting to his eyes alone. So yes recent developments seem to imply this is possible, however Kishi seemed to want to be sure it wasn't actually done by any in the clan.
However, in Sasuke's case, their is strong evidence pointing to the possibility that he simply had Itachi's eyes transferred and his old ones were discarded. Not to mention Itachi's whole plan with Naruto's gift revolved around Sasuke taking his eyes and the Jutsu reacting to his eyes alone. So yes recent developments seem to imply this is possible, however Kishi seemed to want to be sure it wasn't actually done by any in the clan.