Look at it this way: if you were standing in the Temple of Time watching Link pull the Master Sword, you see him go up in that blue light column, and disappear. Very shortly afterwards, you would see the blue light again, and Link would appear, letting go of the Master Sword, which is now in the pedestal again.
this wouldnt happen. Link is sent back to a time before he went to the future and he is sent back by Zelda, not by the power of the master sword. we see him walking up to Zelda in the gardens of the castle where he first met her in the game and this all took place before he was sealed for 7 years, so no, you would not see him reappear putting the master sword in the pedastal.
also, there would not be two links at all. he was not just plain old sent back in time. he is sent back to his original time before anything happened. he is sent back to HIS childhood, not just back to the time of his childhood. it is literally as if nothing had happened and if nothing had happened yet, then there is no future link to go back in time which means there is only one link.