I don't know what to tell you on this problem. Petunias rarely have rotting problems unless they are getting too much moisture. You don't say where these plants are growing (raised bed? standard garden? pots?) so it's hard to guess what's happening. It might be that your plants had problems to begin with and by moving them around, you've just accelerated their demise. I might start with fresh plants in fresh soil and see what happens. But, if you want to repost with more information feel free to do so. We can probably be of more help if we have more insight into what's going on.