I havent tried this yet but been thinking about it for a while now. I was going to try and run the original project, once that was done I would change my bit and just edit the original project file while it was still up in easel. Change everything you dont want beveled to 0 cut depth and everything you want beveled to the cut depth you want the bevel and run the program again, I was going to start with .0625 and just keep running the file going a little deeper until I got he bevel I wanted, also setting the cut to outline and outside path. Im sure it would work the same with a round over bit.
Might be a nice experiment! and this way you dont have to worry about trying to line up 2 different file perfectly!