Just for clarity, in the fish hobby "media" generally means the stuff we put in filters… and “substrate” is the stuff that covers the floor of our tanks… It sounds like you are referring to substrate…
 
 
The simple answer, it’s fine to add new (clean) substrate on top of old substrate…
 
It’s a good idea to thoroughly clean the old substrate before doing so. This is to prevent burying waste where it will rot. The only concern you will have is any bacteria that is living in the surface of the old substrate may be cut off from the flow of water. But it is very unlikely that a large enough percentage of your overall bacterial colony will be negatively effected by doing this.
 
As with any big change we make, it’s always a good idea to do a moderate water change a day or two afterwards to counter any effects you may have caused.
 
 
If I am off base and you do mean adding new bio media on top of old bio media, that’s fine too and has even less concerns…