So basically your question is:
Has converting from your first method of represnting the hash to the second method broken the references judging by the output from Data::Dumper. If so, then the answer is no. dragonchild is right on this one, the Data::Dumper module realises that filehandle of all your cpyXX objects reference the exact same DATA and so these cross-references in Data::Dumper look perfectly valid to me.