I turn on and off the inDesign layers in order to export what ever is on as eps for Illustrator use, sort of manually separating the issues I see to make life easier. Then I open the eps's in Illy and replace into layers that suit my production. Or even delete temporarily, export, revert, delete other bits and export. BTW, the cut and paste method sometimes goofs up. We are always having to edit the files to suit carton dies but this could of course work for labels too. Pkg is fraught with poor preparation by the designers and must be edited, sometimes fully.