If the end result will be good for them (and more space is always good), then do it. They'll get over it.
Also, it really depends on your chickens. Breeds, personalities, how they were raised. Mine grew up with little kids and were present for and observed the entire construction of their run. Also, I had to have their coop relocated last fall and the run heavily modified, so there was a lot of change and construction going on with them right there. They also lived in my basement briefly. So they are very used to loud noises, tools, lots of fuss and mess, and things changing around them. They did just fine through it all. I wouldn't say that they are afraid of change or new things at all. Rather, they seem to be very curious. They are always up in my face examining everything I bring in, trying to peck at the spinning drill bit, climbing on my ladder, patrolling new areas to check them out etc. Only the Barnevelders are a bit reserved at first, but the Orpingtons don't give a cluck and want to see and peck everything new. They are also the first to figure out a new arrangement, how to get in/out and so on. I really can't say if it's a breed thing or how they grew up, but they take change very well (unless the change involves snow... Then they'll complain and refuse to come out

).