Question: What’s the difference between Microsoft.MetadirectoryServices.dll and Microsoft.MetadirectoryServicesEx.dll?
MIIS/ILM code is using the Microsoft.MetadirectoryServices.dll, while FIM is using Microsoft.MetadirectoryServicesEx.dll.
Can the old DLL be removed from the FIM code extensions, when the new DLL is referenced in code?
You should use the Ex.dll when possible. The other DLL is only there in case you have a DLL from MIIS, has lost the sources, and cannot recompile it. The only difference between the two is that Ex is digitally signed and the other is not. When you have changed the references to Ex.dll you will not need the other.