Hmmm. There are two things that need to be unlinked when you save a version: If you're using Assignment files (.icma), you need to delete those from the Assignment panel. When you do that, all the linked stories (.icml) get moved to the Unassigned InCopy Content category in that panel. You select all the stories there and click the Unlink (trashcan) icon at the bottom of the Assignments panel.
Then you do the Save As. Then you jump to the server and delete the old assignment files and incopy stories there, which InDesign does not do.
Then you go back to the ID file and re-export the stories to InCopy Assignments.
With the ID/IC workflow, you're not supposed to be creating versions of the ID file. It kinda defeats the purpose. Once you've made stories editable to InCopy, that's the ID file that ultimately gets packaged for the printer.
If for your own reasons you really need to have versions of the ID file (again, that's a very rare case w/all my IC/ID clients of all sizes), you need to do the whole Clear the Decks routine outlined in the first two paragraphs.
Are you doing that already? It wasn't clear from your description.
AM