How do I change the Views (Entity Reference) filter via AJAX?
I am going to answer my own question in hopes this ccan help someone.  However I am welcome to hear other options :)

What I ended up doing was attach a javascript that updates the autocomplete's path.  Meaning when a user clicks on the checkbox it updates the input box for the autocomplete's attribute. The attribute called data-autocomplete-path.  I appended a query string without messing with the functionality of it.  This extra value gets sent to hook_views_pre_view.  

This worked for me