However, I would like to say that although the chemistry depends largely on the actors, it also is related to the characters. So, if we get Prem back intact, the chemistry will be the same (or who knows, even better), but if we get a humshakal, then something in the essence of the story will somehow die. An example is Karnvir Bohra and Tina Parekh, who were amazing as Prem-Mukti in Kasautii Zindagi Kay. But, when Mukti was killed off, and came back as Devki, me and my friends all felt that the chemistry was no longer the same between the two, even though the actors were the same. Maybe that was also due to the story, but they did not have the magic of Prem-Mukti in them anymore.
Also, we can't really say after a break, because Prem was ALWAYS there. There wasn't one week where he wasn't shown in some form, then there was a 2 week strike, where nobody was shooting. So, I don't think HC and AG had time to miss each other. (although I would be soooo happy if they did). If we take the strike to be a break, then I suppose Heer's dream scene with Prem should be their first scene together (after the break), which was certainly NOT lacking chemistry. lol.