In GC2 you got some production credit when changing out one building for another (e.g. Mfg bld->research bld). In GC3 you first destroy the old building then rebuild the desired one from scratch.
I can understand why you did this and would not mind so much if you got something back when destroying it. If you don’t want to go back to the GC2 method, the simplest may be to provide cash for scrap recovered form buildings destruction. With the adjacency bonus and unpredictable terraforming, there is usually good reason to redo a planets building strategy/layout in mid game and on. It would be nice (and reasonable) to get something back when doing it.