upload.module has the code you'll need to study--specifically,
upload_nodeapi and upload_save.

Note also that when you delete the original node, the original files attached to the cloned node will be deleted as well.

There is work to assign files to user instead of nodes, and afaik this would solve the problem

Philippe

Note that saving file associations is limited by a permission.

The key question to consider is, what does upload do with a *new* node? In
this case, any files associated with a node are those that were just
uploaded.

// New file upload
elseif (strpos($file->fid, 'upload') !== FALSE) {

This won't help you, as your files array doesn't contain this marker.

Consider instead:

elseif ($node->old_vid && is_numeric($fid)) {

You could consider tricking upload.module into doing the handling by setting
an old_vid. Or else just write your own handling based on upload_save.