"by design". that was well understood from the beginning. "To Clone", which is my understanding of the intent, literally means "ALL FILES", not just some or most of them. And, as you yourself inferred, it won't happen because it can't, at least not from WinExpl. anyway.
There's a basic misunderstanding here.
Here's what he OP said:"...is there a program that is available for me to only move certain files over too the new hdd, rather than clone the lot or copy and paste into the hdd...?
Explorer is the program to use.