I am not sure if you can actually merge two different scenery files with any sucess.
Because of the way FS layers scenery it will be hard to merge two areas into one with out creating two objects in the same place. So if you have two different sceneries for one area and want to make just one area out of the two, then the only way I know of would be to make a scenery that had something from each file but you will have to be carefull to make sure that two objects do not occupy the same place.
The biggest problem is to know exactly what is in the scenery and the only way to know that would be to have the source file that was used to create it,and most designers are not willing to let others have there source codes they used to design the scenery with.
Scenery files are BGL files and are compiled from a source file. I do not know of any programs that will decompile a bgl file thus turning it back int a source file that you could edit then recompile it.
