Comment 3 for bug 267565

They way duplicating layer with clones works is as expected. This is the usual way copying works, it's not affected by layers.

When you copy a clone, it keeps the same original as the object it is a copy of.
When you copy an object that is not a clone, it doesn't suddenly become a clone.

In the development builds there is a new feature Relink to copied. You can copy an object, select some clones and use that option.
In Inkscape preferences under Clones there is an option: When duplicating original+clones: Relink duplicated clones. When this option is ticked you get a new identical set of original and its clones. The copy of the original will become a new original, and the copied clones will be clones of the new original.

Are you actually requesting a feature that would turn a copy of an object that has clones into one of its clones?