You can just make N copies of your subpanel VI, either ahead of time (if you want to take care of recopying them when you make changes) or else programmatically, depending on what N value the user selects. Programmatically is probably better, because then you can truly deal with an arbitrary number of copies, and you can also programmatically delete them when you're done.
Instead of trying to load the master VI into each subpanel, just load a copy. You can do all of this in a For Loop, at which point you can instruct the subpanel VIs to run, pass them arguments, etc.
Hope that helps,
John