The 396 and 996 will not clone either direction. Just enough difference that it won't work.
If you are using the Uniden UASD software, however, you can share files. You have to change the default file path so they both use the same folder. This can save you lots of time when you make changes and updates.
Do all your editing with the 996 software. If you save a file from the 396 software, you will lose the fancy differences the 996 file has, like multiple sites, etc.