My first question would be are you planning on keeping different breeds separate in different coops and do you keep roosters? If yes, you may have some problems with cross-breeding if you let them all out into the run at the same time.
Also, if you had plans for all the chickens to stay in different coops at night, you probably wouldn't be able to force them to divide themselves up the way you wanted every night. They might all end up in just one of the coops fighting over the roosts there...
Of course, you could always fix this problem by staggering the times they were allowed out in the run OR you could divide up the current run with additional fencing.
If none of these issues seem like a problem to you, then I'd say go ahead and do it since it would probably save a lot of space.