I know, it is annoying.
Only way I found to get clean copies is by copying the objects directly in the xml-documents.
Save your scenes with a sif extension (sifz is compressed, sif is not). Open both in a text editor (I like to use Scite)
Now in the original scene find the object. It's within a tag starting with <layer type= and then at the end your layer name. Select form this line and all lines to the ending </layer>.
Now paste this in your new scene xml. just after an existing </layer>. Or below >name> if no layers exists.
Now you've copied the object, but it still links to an exported value that we also need to copy. It resides in the <defs> tag at the beginning of the document.
For an exported origin in my test file it looks like this:
If you already have a <defs> tag copy the vector id tag, else copy the defs also.
Done, now you have an independent copy that links to an exported value in its own scene.