I was worried about changing the substrate in my two's vivs when i seperated them. They were on Calci Sand and were licking it all the time so I decided to switch pronto when we seperated the two of them. We did it one night and they didn't seem to mind much. They are on newspaper now until their new vivs are built (if the b/f ever gets off his duff) where we will be putting some slate tiles in for them. The female we have to be careful not to put any coloured newsprint in her tank as she thinks all the green paper is food and tries to eat it.
Sure, they were stressed a little, but overall their health matters the most, so I would just go ahead and do it. Good luck!